Methods, Reagents And Cells For Biosynthesizing Compound

Abstract

This document describes biochemical pathways for producing 2(E)-heptenedioyl-CoA methyl ester from precursors such as 2-oxo-glutarate, acetyl-CoA, or succinyl-CoA using one or more of a fatty acid O-methyltransferase, a thioesterase, a CoA-transferase, a CoA ligase, as well as recombinant hosts expressing one or more of such enzymes. 2(E)-heptenedioyl-CoA methyl ester can be enzymatically converted to pimeloyl-CoA using a trans-2-enoyl-CoA reductase, and a methylesterase. Pimeloyl-CoA can be enzymatically converted to pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, or 1,7-heptanediol.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Application Nos. 62/012,674 and 62/012,735, both of which were filed on Jun. 16, 2014, the disclosures of which are incorporated by reference herein in their entireties.

TECHNICAL FIELD

[0002] This invention relates to methods of shielding a carbon chain aliphatic backbone, functionalized with terminal carboxyl groups, in a recombinant host using a polypeptide having the activity of a fatty acid O-methyltransferase. This invention also relates to methods for biosynthesizing heptenedioyl-CoA methyl ester in a host using one or more of (i) a polypeptide having fatty acid O-methyltransferase activity (ii) a polypeptide having thioesterase activity or CoA-transferase activity, or (iii) a polypeptide having CoA ligase activity, and to recombinant host cells expressing one or more such enzymes. In addition, this invention also relates to methods for enzymatically converting hept-2-enedioyl-CoA methyl ester to pimeloyl-CoA using a polypeptide having trans-enoyl-CoA reductase activity and/or a polypeptide having pimeloyl-[acp]methyl ester esterase activity, and enzymatically converting pimeloyl-CoA to one or more of pimelic acid, 7-aminoheptanoic acid, heptamethylenediamine, 7-hydroxyheptanoic acid, and 1,7-heptanediol (hereafter "C7 building blocks"), and recombinant hosts that produce such C7 building blocks.

BACKGROUND

[0003] Nylons are polyamides which are sometimes synthesized by the condensation polymerisation of a diamine with a dicarboxylic acid. Similarly, nylons may be produced by the condensation polymerisation of lactams. A ubiquitous nylon is Nylon 6,6, which is produced by reaction of hexamethylenediamine (HMD) and adipic acid. Nylon 6 is produced by a ring opening polymerisation of caprolactam (Anton & Baird, Polyamides Fibers, Encyclopedia of Polymer Science and Technology, 2001).

[0004] Nylon 7 and Nylon 7,7 represent novel polyamides with value-added characteristics compared to Nylon 6 and Nylon 6,6. Nylon 7 is produced by polymerisation of 7-aminoheptanoic acid, whereas Nylon 7,7 is produced by condensation polymerisation of pimelic acid and heptamethylenediamine. No economically viable petrochemical routes exist to producing the monomers for Nylon 7 and Nylon 7,7.

[0005] Given no economically viable petrochemical monomer feedstocks, biotechnology offers an alternative approach via biocatalysis. Biocatalysis is the use of biological catalysts, such as enzymes, to perform biochemical transformations of organic compounds.

[0006] Both bioderived feedstocks and petrochemical feedstocks are viable starting materials for the biocatalysis processes.

[0007] Accordingly, against this background, it is clear that there is a need for methods for producing pimelic acid, 7-aminoheptanoic acid, heptamethylenediamine, 7-hydroxyheptanoic acid and 1,7-heptanediol (hereafter "C7 building blocks") wherein the methods are biocatalyst-based.

[0008] However, no wild-type prokaryote or eukaryote naturally overproduces or excretes C7 building blocks to the extracellular environment. Nevertheless, the metabolism of pimelic acid has been reported.

[0009] The dicarboxylic acid, pimelic acid, is converted efficiently as a carbon source by a number of bacteria and yeasts via .beta.-oxidation into central metabolites. .beta.-oxidation of CoEnzyme A (CoA) activated pimelate to CoA-activated 3-oxopimelate facilitates further catabolism via, for example, pathways associated with aromatic substrate degradation. The catabolism of 3-oxopimeloyl-CoA to acetyl-CoA and glutaryl-CoA by several bacteria has been characterized comprehensively (Harwood and Parales, Annual Review of Microbiology, 1996, 50, 553-590).

[0010] The optimality principle states that microorganisms regulate their biochemical networks to support maximum biomass growth. Beyond the need to express heterologous pathways in a host organism, directing carbon flux towards C7 building blocks that serve as carbon sources rather than to biomass growth constituents, contradicts the optimality principle. For example, transferring the 1-butanol pathway from Clostridium species into other production strains has often fallen short by an order of magnitude compared to the production performance of native producers (Shen et al., Appl. Environ. Microbiol., 2011, 77(9), 2905-2915).

[0011] The efficient synthesis of the seven carbon aliphatic backbone precursor is a key consideration in synthesizing C7 building blocks prior to forming terminal functional groups, such as carboxyl, amine or hydroxyl groups, on the C7 aliphatic backbone.

SUMMARY

[0012] This document is based at least in part on the discovery that it is possible to construct biochemical pathways via hept-2-enedioyl-CoA (also referred to as 2-heptenedioyl-CoA)methyl ester for producing a seven carbon chain aliphatic backbone precursor such as pimeloyl-CoA, in which one or two functional groups, i.e., carboxyl, amine, or hydroxyl, can be formed, leading to the synthesis of one or more of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol (hereafter "C7 building blocks). Pimelic acid and pimelate, 7-hydroxyheptanoic acid and 7-hydroxyheptanoate, and 7-aminoheptanoic and 7-aminoheptanoate are used interchangeably herein to refer to the compound in any of its neutral or ionized forms, including any salt forms thereof. It is understood by those skilled in the art that the specific form will depend on pH. These pathways, metabolic engineering and cultivation strategies described herein rely on producing 2(E)-heptenedioate methyl ester from 2(E)-heptenedioate using, for example, a fatty acid O-methyltransferase and producing 2(E)-heptenedioyl-CoA methyl ester from 2(E)-heptenedioate methyl ester using, for example, a CoA ligase. Pimeloyl-CoA can be produced from 2(E)-heptenedioyl-CoA methyl ester using, for example, a trans-2-enoyl-CoA reductase and a pimelyl-[acp]methyl ester esterase. 2(E)-heptenedioate can be produced, for example, from 2-oxoglutarate, acetyl-CoA or succinate semialdehyde as shown in FIGS. 1, 2, and 3, respectively.

[0013] In the face of the optimality principle, it surprisingly has been discovered that appropriate non-natural pathways, feedstocks, host microorganisms, attenuation strategies to the host's biochemical network and cultivation strategies may be combined to efficiently produce one or more C7 building blocks.

[0014] In some embodiments, a terminal carboxyl group can be enzymatically formed using a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 5-oxopentanoate dehydrogenase, a reversible CoA-ligase (e.g., a reversible succinyl-CoA-ligase), or a CoA-transferase (e.g., a glutaconate CoA-transferase). See, FIG. 4.

[0015] In some embodiments, a terminal amine group can be enzymatically formed using a .omega.-transaminase or a deacetylase. See, FIGS. 5 and 6.

[0016] In some embodiments, a terminal hydroxyl group can be enzymatically formed using a 4-hydroxybutyrate dehydrogenase, 5-hydroxypentanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, or an alcohol dehydrogenase. See, FIGS. 7 and 8.

[0017] The two terminal functional groups can be the same (e.g., amine or hydroxyl) or can be different (e.g., a terminal amine and a terminal carboxyl group; or a terminal hydroxyl group and a terminal carboxyl group).

[0018] Any of the methods can be performed in a recombinant host by fermentation. The host can be subjected to a cultivation strategy under anaerobic, micro-aerobic or mixed oxygen/denitrification cultivation conditions. The host can be cultured under conditions of nutrient limitation. The host can be retained using a ceramic membrane to maintain a high cell density during fermentation. The final electron acceptor can be an alternative to oxygen such as nitrates.

[0019] In any of the methods, the host's tolerance to high concentrations of a C7 building block can be improved through continuous cultivation in a selective environment.

[0020] The principal carbon source fed to the fermentation can derive from biological or non-biological feedstocks. In some embodiments, the biological feedstock is, includes, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.

[0021] In some embodiments, the non-biological feedstock is or derives from natural gas, syngas, CO.sub.2/H.sub.2, methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cyclohexane oxidation processes, or a terephthalic acid/isophthalic acid mixture waste stream.

[0022] This document features a recombinant host that includes at least one exogenous nucleic acid encoding (i) a fatty acid O-methyltransferase; and (ii) a thioesterase or CoA-transferase, the host producing 2(E)-heptenedioate methyl ester. The host can further include an exogenous CoA ligase, the host further producing 2(E)-heptenedioyl-CoA methyl ester. In some embodiments, the host can further include an exogenous trans-2-enoyl-CoA reductase and/or an exogenous pimeloyl-[acp]methyl ester methylesterase, and produce pimeloyl-CoA.

[0023] This document also features a recombinant host that includes at least one exogenous nucleic acid encoding (i) a fatty acid O-methyltransferase; and (ii) a CoA ligase, the host producing 2(E)-heptenedioyl-CoA methyl ester. Such a host further can include an exogenous thioesterase or CoA-transferase. In some embodiments, the host can further include an exogenous trans-2-enoyl-CoA reductase and/or an exogenous pimeloyl-[acp]methyl ester methylesterase, and produce pimeloyl-CoA.

[0024] A recombinant host producing pimeloyl-CoA further can include at least one exogenous nucleic acid encoding one or more of a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 5-oxopentanoate dehydrogenase, a CoA-transferase, a reversible CoA-ligase (e.g., a reversible succinyl-CoA-ligase), an acetylating aldehyde dehydrogenase, or a carboxylate reductase, the host producing pimelic acid or pimelate semialdehyde. In any of the recombinant hosts expressing a carboxylate reductase, a phosphopantetheinyl transferase also can be expressed to enhance the activity of the carboxylate reductase.

[0025] A recombinant host producing pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a .omega.-transaminase, and further produce 7-aminoheptanoate.

[0026] A recombinant host producing pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a 4-hydroxybutyrate dehydrogenase, a 5-hydroxypentanoate dehydrogenase or a 6-hydroxyhexanoate dehydrogenase, the host further producing 7-hydroxyheptanoic acid.

[0027] A recombinant host producing pimelate semialdehyde, 7-aminoheptanoate, or 7-hydroxyheptanoic acid further can include a carboxylate reductase, a .omega.-transaminase, a deacetylase, an N-acetyl transferase, or an alcohol dehydrogenase, the host further producing heptamethylenediamine.

[0028] A recombinant host producing 7-hydroxyheptanoic acid further can include at least one exogenous nucleic acid encoding a carboxylate reductase or an alcohol dehydrogenase, the host further producing 1,7-heptanediol.

[0029] The recombinant host can be a prokaryote, e.g., from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia acidovorans, from the genus Bacillus such as Bacillus subtillis; from the genes Lactobacillus such as Lactobacillus delbrueckii; from the genus Lactococcus such as Lactococcus lactis or from the genus Rhodococcus such as Rhodococcus equi.

[0030] The recombinant host can be an eukaryote, e.g., a eukaryote from the genus Aspergillus such as Aspergillus niger; from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; from the genus Yarrowia such as Yarrowia lipolytica, from the genus Issatchenkia such as Issathenkia orientalis, from the genus Debaryomyces such as Debaryomyces hansenii, from the genus Arxula such as Arxula adenoinivorans, or from the genus Kluyveromyces such as Kluyveromyces lactis.

[0031] Any of the recombinant hosts described herein further can include one or more of the following attenuated enzymes: polyhydroxyalkanoate synthase, an acetyl-CoA thioesterase, an acetyl-CoA specific .beta.-ketothiolase, a phosphotransacetylase forming acetate, an acetate kinase, a lactate dehydrogenase, a menaquinol-fumarate oxidoreductase, an alcohol dehydrogenase forming ethanol, a triose phosphate isomerase, a pyruvate decarboxylase, a glucose-6-phosphate isomerase, a transhydrogenase dissipating the NADPH imbalance, an glutamate dehydrogenase dissipating the NADPH imbalance, a NADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoA dehydrogenase; an acyl-CoA dehydrogenase accepting C7 building blocks and central precursors as substrates; a glutaryl-CoA dehydrogenase; or a pimeloyl-CoA synthetase.

[0032] Any of the recombinant hosts described herein further can overexpress one or more genes encoding: an acetyl-CoA synthetase, a 6-phosphogluconate dehydrogenase; a transketolase; a puridine nucleotide transhydrogenase; a formate dehydrogenase; a glyceraldehyde-3P-dehydrogenase; a malic enzyme; a glucose-6-phosphate dehydrogenase; a fructose 1,6 diphosphatase; a L-alanine dehydrogenase; a PEP carboxylase, a pyruvate carboxylase, PEP carboxykinase, PEP synthase, a L-glutamate dehydrogenase specific to the NADPH used to generate the imbalance; a methanol dehydrogenase, a formaldehyde dehydrogenase, a lysine transporter; a dicarboxylate transporter; an S-adenosylmethionine synthetase, a 3-phosphoglycerate dehydrogenase, a 3-phosphoserine aminotransferase, a phosphoserine phosphatase, and/or a multidrug transporter.

[0033] The reactions of the pathways described herein can be performed in one or more cell (e.g., host cell) strains (a) naturally expressing one or more relevant enzymes, (b) genetically engineered to express one or more relevant enzymes, or (c) naturally expressing one or more relevant enzymes and genetically engineered to express one or more relevant enzymes. Alternatively, relevant enzymes can be extracted from any of the above types of host cells and used in a purified or semi-purified form. Extracted enzymes can optionally be immobilized to a solid substrate such as the floors and/or walls of appropriate reaction vessels. Moreover, such extracts include lysates (e.g., cell lysates) that can be used as sources of relevant enzymes. In the methods provided by the document, all the steps can be performed in cells (e.g., host cells), all the steps can be performed using extracted enzymes, or some of the steps can be performed in cells and others can be performed using extracted enzymes.

[0034] Many of the enzymes described herein catalyze reversible reactions, and the reaction of interest may be the reverse of the described reaction. The schematic pathways shown in FIGS. 1 to 8 illustrate the reaction of interest for each of the intermediates.

[0035] In one aspect, this document features a method for producing a bioderived seven carbon compound. The method for producing a bioderived seven carbon compound can include culturing or growing a recombinant host as described herein under conditions and for a sufficient period of time to produce the bioderived seven carbon compound, wherein, optionally, the bioderived seven carbon compound is selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, 1,7-heptanediol, and combinations thereof.

[0036] In one aspect, this document features composition comprising a bioderived seven carbon compound as described herein and a compound other than the bioderived seven carbon compound, wherein the bioderived seven carbon compound is selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, 1,7-heptanediol, and combinations thereof. For example, the bioderived seven carbon compound is a cellular portion of a host cell or an organism.

[0037] This document also features a biobased polymer comprising the bioderived pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, 1,7-heptanediol, and combinations thereof.

[0038] This document also features a biobased resin comprising the bioderived pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, 1,7-heptanediol, and combinations thereof, as well as a molded product obtained by molding a biobased resin.

[0039] In another aspect, this document features a process for producing a biobased polymer that includes chemically reacting the bioderived pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, or 1,7-heptanediol, with itself or another compound in a polymer producing reaction.

[0040] In another aspect, this document features a process for producing a biobased resin that includes chemically reacting the bioderived pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, or 1,7-heptanediol, with itself or another compound in a resin producing reaction.

[0041] Also, described herein is a biochemical network comprising a polypeptide having fatty acid O-methyltransferase activity, wherein the polypeptide having fatty acid O-methyltransferase activity enzymatically converts 2(E) heptenedioic acid to 2(E) heptenedioate methyl ester. The biochemical network can further include a polypeptide having CoA ligase activity, wherein the polypeptide having CoA ligase activity enzymatically converts 2(E) heptenedioate methyl ester to 2(E) heptenedioyl-CoA methyl ester. The biochemical network can further include a polypeptide having trans-2-enoyl-CoA reductase activity, wherein the polypeptide having trans-2-enoyl-CoA reductase activity enzymatically converts 2(E) heptenedioyl-CoA methyl ester to pimeloyl-CoA methyl ester. The biochemical network can further include a polypeptide having pimelyl-[acp]methyl ester esterase activity, wherein the polypeptide having pimelyl-[acp]methyl ester esterase activity enzymatically converts pimeloyl-CoA methyl ester to pimeloyl-CoA.

[0042] The biochemical network can further include one or more polypeptides having thioesterase, reversible CoA-ligase, glutaconate CoA-transferase, .omega.-transaminase, 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, alcohol dehydrogenase, carboxylate reductase, or alcohol dehydrogenase activity, wherein the one or more polypeptides having thioesterase, reversible CoA-ligase, glutaconate CoA-transferase, .omega.-transaminase, 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, alcohol dehydrogenase, carboxylate reductase, or alcohol dehydrogenase activity enzymatically convert pimeloyl-CoA to a product selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol.

[0043] Also, described herein is a means for obtaining 2(E)-heptenedioate methyl ester, 2-heptenedioyl-CoA methyl ester, pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol using one or more polypeptides having thioesterase, reversible CoA-ligase, glutaconate CoA-transferase, .omega.-transaminase, 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, alcohol dehydrogenase, carboxylate reductase or alcohol dehydrogenase activity.

[0044] In another aspect, this document features a composition comprising one or more polypeptides having fatty acid O-methyltransferase, thioesterase, reversible CoA-ligase, glutaconate CoA-transferase, .omega.-transaminase, 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, alcohol dehydrogenase, carboxylate reductase, or alcohol dehydrogenase activity and at least one of 2(E)-heptenedioate methyl ester, 2-heptenedioyl-CoA methyl ester, pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol. The composition can be cellular.

[0045] One of skill in the art understands that compounds containing carboxylic acid groups (including, but not limited to, organic monoacids, hydroxyacids, aminoacids, and dicarboxylic acids) are formed or converted to their ionic salt form when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include, but are not limited to, ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. A salt of the present invention is isolated as a salt or converted to the free acid by reducing the pH to below the pKa, through addition of acid or treatment with an acidic ion exchange resin.

[0046] One of skill in the art understands that compounds containing amine groups (including, but not limited to, organic amines, aminoacids, and diamines) are formed or converted to their ionic salt form, for example, by addition of an acidic proton to the amine to form the ammonium salt, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids including, but not limited to, acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4'-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. A salt of the present invention is isolated as a salt or converted to the free amine by raising the pH to above the pKb through addition of base or treatment with a basic ion exchange resin.

[0047] One of skill in the art understands that compounds containing both amine groups and carboxylic acid groups (including, but not limited to, aminoacids) are formed or converted to their ionic salt form by either 1) acid addition salts, formed with inorganic acids including, but not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids including, but not limited to, acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4'-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like, or 2) when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include, but are not limited to, ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. A salt can of the present invention is isolated as a salt or converted to the free acid by reducing the pH to below the pKa through addition of acid or treatment with an acidic ion exchange resin.

[0048] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein including GenBank and NCBI submissions with accession numbers are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

[0049] The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and the drawings, and from the claims. The word "comprising" in the claims may be replaced by "consisting essentially of" or with "consisting of" according to standard practice in patent law.

DESCRIPTION OF DRAWINGS

[0050] FIG. 1 is a schematic of exemplary biochemical pathways leading to pimeloyl-CoA from 2-oxo-glutarate or acetyl-CoA, via a hept-2-enedioyl-CoA methyl ester.

[0051] FIG. 2 is a schematic of an exemplary biochemical pathway leading to pimeloyl-CoA from 2-oxo-glutarate via a hept-2-enedioyl-CoA methyl ester.

[0052] FIG. 3 is a schematic of exemplary biochemical pathways leading to pimeloyl-CoA from succinyl-CoA or 2-oxo-glutarate via a hept-2-enedioyl-CoA methyl ester.

[0053] FIG. 4 is schematic of exemplary biochemical pathways leading to pimelic acid using pimeloyl-CoA as a central precursor.

[0054] FIG. 5 is a schematic of exemplary biochemical pathways leading to 7-aminoheptanoate using pimeloyl-CoA or pimelate as a central precursor.

[0055] FIG. 6 is a schematic of exemplary biochemical pathways leading to heptamethylenediamine using 7-aminoheptanoate, 7-hydroxyheptanoate, or pimelate semialdehyde as a central precursor.

[0056] FIG. 7 is a schematic of exemplary biochemical pathways leading to 7-hydroxyheptanoate using pimelate, pimeloyl-CoA or pimelate semialdehyde as a central precursor.

[0057] FIG. 8 is a schematic of an exemplary biochemical pathway leading to 1,7-heptanediol using 7-hydroxyheptanoate as a central precursor.

[0058] FIG. 9 contains the amino acid sequences of a Mycobacterium marinum fatty acid O-methyltransferase (GenBank Accession No. ACC41782.1; SEQ ID NO: 1), a Mycobacterium smegmatis str. MC2 fatty acid O-methyltransferase (GenBank Accession No. ABK73223.1; SEQ ID NO: 2), a Pseudomonas putida fatty acid O-methyltransferase (GenBank Accession No. CAA39234.1; SEQ ID NO: 3), a Lactobacillus brevis acyl-[acp]thioesterase (GenBank Accession No. ABJ63754.1, SEQ ID NO: 4), a Lactobacillus plantarum acyl-[acp]thioesterase (GenBank Accession No. CCC78182.1, SEQ ID NO: 5), an Escherichia coli pimelyl-[acp]methyl ester esterase (see GenBank Accession No. AAC76437.1, SEQ ID NO: 6), a Mycobacterium marinum carboxylate reductase (See Genbank Accession No. ACC40567.1, SEQ ID NO: 7), a Mycobacterium smegmatis carboxylate reductase (See Genbank Accession No. ABK71854.1, SEQ ID NO: 8), a Segniliparus rugosus carboxylate reductase (See Genbank Accession No. EFV11917.1, SEQ ID NO: 9), a Mycobacterium smegmatis carboxylate reductase (See Genbank Accession No. ABK75684.1, SEQ ID NO: 10), a Mycobacterium massiliense carboxylate reductase (See Genbank Accession No. EIV11143.1, SEQ ID NO: 11), a Segniliparus rotundus carboxylate reductase (See Genbank Accession No. ADG98140.1, SEQ ID NO: 12), a Chromobacterium violaceum .omega.-transaminase (See Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas aeruginosa .omega.-transaminase (See Genbank Accession No. AAG08191.1, SEQ ID NO: 14), a Pseudomonas syringae .omega.-transaminase (See Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides .omega.-transaminase (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), an Escherichia coli .omega.-transaminase (see Genbank Accession No. AAA57874.1, SEQ ID NO: 17), a Vibrio fluvialis .omega.-transaminase (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18), a Bacillus subtilis phosphopantetheinyl transferase (see Genbank Accession No. CAA44858.1, SEQ ID NO: 19), a Nocardia sp. NRRL 5646 phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1, SEQ ID NO: 20), an Escherichia coli thioesterase encoded by tesB (See GenBank Accession No. AAA24665.1, SEQ ID NO: 21), an Escherichia coli long-chain-fatty-acid-CoA ligase (Genbank Accession No. CAA50321.1, SEQ ID NO: 22), a Cupriavidus necator long-chain-fatty-acid-CoA ligase (Genbank Accession No. CAJ95550.1, SEQ ID NO: 23), an Acidaminococcus fermentans glutaconate CoA-transferase (see, e.g., Genbank Accession No. CAA57199.1 (GctA) and CAA57200.1 (GctB), SEQ ID NOs: 24 and 25, respectively), a Treponema denticola enoyl-CoA reductase (see, e.g., Genbank Accession No. AAS11092.1, SEQ ID NO: 26), an Euglena gracilis enoyl-CoA reductase (see, e.g., Genbank Accession No. AAW66853.1, SEQ ID NO: 27), a Pseudomonas reinekei MT1 .beta.-ketothiolase (see, e.g., Genbank Accession No. ACZ63623.1, SEQ ID NO: 28), a Pseudomonas putida .beta.-ketothiolase (see, e.g., Genbank Accession No. AAA85138.1, SEQ ID NO: 29), a Burkholderia xenovorans .beta.-ketothiolase (see, e.g., Genbank Accession No. ABE33819.1, SEQ ID NO: 30), an Arthrobacter sp. .beta.-ketothiolase (see, e.g., Genbank Accession No. ABK03524.1, SEQ ID NO: 31), a Burkholderia xenovorans .beta.-ketothiolase (see, e.g., Genbank Accession No. ABE36495.1, SEQ ID NO: 32), a Geobacillus kaustophilus .beta.-ketothiolase (see, e.g., Genbank Accession No. BAD75605.1, SEQ ID NO: 33), a Gordonia bronchialis .beta.-ketothiolase (see, e.g., Genbank Accession ACY20886.1, SEQ ID NO: 34), a Citrobacter freundii .beta.-ketothiolase (see, e.g., Genbank Accession KFB98168.1, SEQ ID NO: 35), a Burkholderia sp. .beta.-ketothiolase (see, e.g., Genbank Accession ADG18081.1, SEQ ID NO: 36), a Beijerinckia indica .beta.-ketothiolase (see, e.g., Genbank Accession ACB95386.1, SEQ ID NO: 37), an Arthrobacter arilaitensis .beta.-ketothiolase (see, e.g., Genbank Accession CBT74677.1, SEQ ID NO: 38), a Cupriavidus necator .beta.-ketothiolase (see, e.g., Genbank Accession AAC38322.1, SEQ ID NO: 39), and an Escherichia coli .beta.-ketothiolase (see, e.g., Genbank Accession AAC74479.1, SEQ ID NO: 40).

[0059] FIG. 10 is a bar graph of the relative absorbance at 412 nm after 20 minutes of released CoA as a measure of the activity of a thioesterase for converting pimeloyl-CoA to pimelate relative to the empty vector control.

[0060] FIG. 11 is a bar graph summarizing the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of carboxylate reductases relative to the enzyme only controls (no substrate).

[0061] FIG. 12 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of carboxylate reductases for converting pimelate to pimelate semialdehyde relative to the empty vector control.

[0062] FIG. 13 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of carboxylate reductases for converting 7-hydroxyheptanoate to 7-hydroxyheptanal relative to the empty vector control.

[0063] FIG. 14 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of carboxylate reductases for converting N7-acetyl-7-aminoheptanoate to N7-acetyl-7-aminoheptanal relative to the empty vector control.

[0064] FIG. 15 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of carboxylate reductases for converting pimelate semialdehyde to heptanedial relative to the empty vector control.

[0065] FIG. 16 is a bar graph summarizing the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the .omega.-transaminase activity of the enzyme only controls (no substrate).

[0066] FIG. 17 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the .omega.-transaminase activity for converting 7-aminoheptanoate to pimelate semialdehyde relative to the empty vector control.

[0067] FIG. 18 is a bar graph of the percent conversion after 4 hours of L-alanine to pyruvate (mol/mol) as a measure of the .omega.-transaminase activity for converting pimelate semialdehyde to 7-aminoheptanoate relative to the empty vector control.

[0068] FIG. 19 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the .omega.-transaminase activity for converting heptamethylenediamine to 7-aminoheptanal relative to the empty vector control.

[0069] FIG. 20 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the .omega.-transaminase activity for converting N7-acetyl-1,7-diaminoheptane to N7-acetyl-7-aminoheptanal relative to the empty vector control.

[0070] FIG. 21 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the .omega.-transaminase activity for converting 7-aminoheptanol to 7-oxoheptanol relative to the empty vector control.

[0071] FIG. 22 is a table of the conversion after 1 hour of pimeloyl-CoA methyl ester to pimeloyl-CoA by a pimeloyl-[acp]methyl ester methylesterase.

[0072] FIG. 23 is a table of the conversion after three hours of glutaryl-CoA and acetyl-CoA to 3-keotpimeloyl-CoA by a .beta.-ketothiolase.

DETAILED DESCRIPTION

[0073] This document provides enzymes, non-natural pathways, cultivation strategies, feedstocks, host microorganisms and attenuations to the host's biochemical network, which generates a seven carbon chain aliphatic backbone from central metabolites in which one or two terminal functional groups may be formed leading to the synthesis of pimelic acid, 7-aminoheptanoic acid, heptamethylenediamine, 7-hydroxyheptanoic acid, or 1,7-heptanediol (referred to as "C7 building blocks" herein). As used herein, the term "central precursor" is used to denote any metabolite in any metabolic pathway shown herein leading to the synthesis of a C7 building block. The term "central metabolite" is used herein to denote a metabolite that is produced in all microorganisms to support growth.

[0074] Host microorganisms described herein can include endogenous pathways that can be manipulated such that one or more C7 building blocks can be produced. In an endogenous pathway, the host microorganism naturally expresses all of the enzymes catalyzing the reactions within the pathway. A host microorganism containing an engineered pathway does not naturally express all of the enzymes catalyzing the reactions within the pathway but has been engineered such that all of the enzymes within the pathway are expressed in the host.

[0075] The term "exogenous" as used herein with reference to a nucleic acid (or a protein) and a host refers to a nucleic acid that does not occur in (and cannot be obtained from) a cell of that particular type as it is found in nature or a protein encoded by such a nucleic acid. Thus, a non-naturally-occurring nucleic acid is considered to be exogenous to a host once in the host. It is important to note that non-naturally-occurring nucleic acids can contain nucleic acid subsequences or fragments of nucleic acid sequences that are found in nature provided the nucleic acid as a whole does not exist in nature. For example, a nucleic acid molecule containing a genomic DNA sequence within an expression vector is non-naturally-occurring nucleic acid, and thus is exogenous to a host cell once introduced into the host, since that nucleic acid molecule as a whole (genomic DNA plus vector DNA) does not exist in nature. Thus, any vector, autonomously replicating plasmid, or virus (e.g., retrovirus, adenovirus, or herpes virus) that as a whole does not exist in nature is considered to be non-naturally-occurring nucleic acid. It follows that genomic DNA fragments produced by PCR or restriction endonuclease treatment as well as cDNAs are considered to be non-naturally-occurring nucleic acid since they exist as separate molecules not found in nature. It also follows that any nucleic acid containing a promoter sequence and polypeptide-encoding sequence (e.g., cDNA or genomic DNA) in an arrangement not found in nature is non-naturally-occurring nucleic acid. A nucleic acid that is naturally-occurring can be exogenous to a particular host microorganism. For example, an entire chromosome isolated from a cell of yeast x is an exogenous nucleic acid with respect to a cell of yeast y once that chromosome is introduced into a cell of yeast y.

[0076] In contrast, the term "endogenous" as used herein with reference to a nucleic acid (e.g., a gene) (or a protein) and a host refers to a nucleic acid (or protein) that does occur in (and can be obtained from) that particular host as it is found in nature. Moreover, a cell "endogenously expressing" a nucleic acid (or protein) expresses that nucleic acid (or protein) as does a host of the same particular type as it is found in nature. Moreover, a host "endogenously producing" or that "endogenously produces" a nucleic acid, protein, or other compound produces that nucleic acid, protein, or compound as does a host of the same particular type as it is found in nature.

[0077] For example, depending on the host and the compounds produced by the host, a recombinant host can express an exogenous polypeptide having fatty acid O-methyltransferase activity.

[0078] For example, depending on the host and the compounds produced by the host, one or more of the following polypeptides may be expressed in the host in addition to a polypeptide having (i) fatty acid O-methyltransferase activity, (ii) thioesterase activity or a CoA-transferase activity, and (iii) CoA ligase activity: a pimelyl-[acp]methyl ester esterase, a (homo).sub.ncitrate synthase, a (homo).sub.ncitrate dehydratase, a (homo)aconitate hydratase, an iso(homo).sub.ncitrate dehydrogenase, an decarboxylase such as an indolepyruvate decarboxylase, a .beta.-ketothiolase, an acetyl-carboxylase, an acetoacetyl-CoA synthase, a 3-hydroxybutyryl-CoA dehydrogenase, an enoyl-CoA hydratase, a glutaryl-CoA dehydrogenase, an enoyl-CoA reductase, a trans-2-enoyl-CoA reductase, a glutaconyl-CoA decarboxylase, a .beta.-ketoacyl-[acp]synthase, a 3-hydroxybutyryl-CoA dehydrogenase, a 2-hydroxyglutarate dehydrogenase, a 2-hydroxyglutaryl-CoA dehydratase, a glutarate semialdehyde dehydrogenase, a 4-hydroxy-2-oxoheptanedioate aldolase, a 2-oxo-hept-3-ene-1,7-dioate hydratase, a 2-enoate reductase, a 2-hydroxyglutarate dehydrogenase, a 2-hydroxyglutaryl-CoA dehydratase, a thioesterase, an aldehyde dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, a reversible CoA-ligase (e.g., a reversible succinyl-CoA-ligase), a CoA-transferase (e.g., a glutaconate CoA-transferase), an acetylating aldehyde dehydrogenase, a carboxylate reductase, 4-hydroxybutyrate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, a .omega.-transaminase, a N-acetyl transferase, an alcohol dehydrogenase, or a deacetylase. In recombinant hosts expressing a carboxylate reductase, a phosphopantetheinyl transferase also can be expressed as it enhances activity of the carboxylate reductase.

[0079] For example, a recombinant host can include at least one exogenous nucleic acid encoding a (i) fatty acid O-methyltransferase, (ii) a thioesterase or CoA-transferase, and/or (iii) a CoA ligase. In some embodiments, a recombinant host includes an exogenous nucleic acid encoding a (i) fatty acid O-methyltransferase and a (ii) thioesterase or CoA-transferase, wherein the host produces 2(E)-heptenedioate methyl ester. In some embodiments, a recombinant host includes an exogenous nucleic acid encoding a fatty acid O-methyltransferase and a CoA ligase, wherein the host produces hept-2-enedioyl CoA methyl ester. In some embodiments, the recombinant host includes an exogenous nucleic acid encoding (i) a fatty acid O-methyltransferase, (ii) a thioesterase, and (iii) a CoA ligase, and produces hept-2-enedioyl CoA methyl ester. Such a host further can include an exogenous trans-2-enoyl-CoA reductase and an exogenous pimeloyl-[acp]methyl ester methylesterase, and further produce pimeloyl-CoA.

[0080] In some embodiments, the host can include one or more of the following exogenous enzymes used to produce glutaryl-CoA from 2-oxo-glutarate: (a) a homocitrate synthase, (b) a homocitrate dehydratase, (c) a homoaconitate hydratase, an (d) isohomocitrate dehydrogenase, (e) a decarboxylase such as indolepyruvate decarboxylase, (f) a glutarate-semialdehyde dehydrogenase, and (g) a glutarate:CoA ligase or CoA-transferase.

[0081] In some embodiments, the host can include one or more of the following exogenous enzymes used to produce glutaryl CoA from acetyl CoA: (a) a .beta.-ketothiolase or an acetyl-carboxylase in combination with an acetoacetyl-CoA synthase, (b) a 3-hydroxybutyryl-CoA dehydrogenase, (c) an enoyl-CoA hydratase, and either (d) a glutaryl-CoA dehydrogenase in combination with an enoyl-CoA reductase or (e) a glutaconyl-CoA decarboxylase.

[0082] In some embodiments, the host can include one or more of the following exogenous enzymes used to produce 2-heptenedioyl-CoA from glutaryl CoA: a .beta.-ketoacyl-[acp]synthase or .beta.-ketothiolase, a 3-hydroxyacyl-CoA dehydrogenase, and an enoyl-CoA hydratase.

[0083] In some embodiments, the host can include one or more of the following exogenous enzymes used to convert 2-oxo-glutarate to hept-2-enedioyl-CoA via 2-oxo-pimelate as shown in FIG. 2: a homocitrate synthase, a homocitrate dehydratase, a homoaconitate hydratase, an isohomocitrate dehydrogenase, a 2-hydroxyglutarate dehydrogenase, a glutaconate CoA-transferase, and a 2-hydroxyglutaryl-CoA dehydratase.

[0084] In some embodiments, the host can include one or more of the following exogenous enzymes used to convert succinate semialdehyde to hept-2-enedioyl-CoA via 2-oxo-pimelate as shown in FIG. 3: a glutarate semialdehyde dehydrogenase, a 4-hydroxy-2-oxoheptanedioate aldolase, a 2-oxo-hept-3-ene-1,7-dioate hydratase, a 2-enoate reductase, a 2-hydroxyglutarate dehydrogenase, a glutaconate CoA-transferase, and a 2-hydroxyglutaryl-CoA dehydratase.

[0085] Such recombinant hosts further can include at least one exogenous nucleic acid encoding one or more of a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 5-oxopentanoate dehydrogenase, a CoA-transferase, a reversible CoA-ligase, an acetylating aldehyde dehydrogenase, or a carboxylate reductase and produce pimelic acid or pimelate semialdehyde. For example, a recombinant host producing pimeloyl-CoA further can include a thioesterase, a reversible Co-ligase (e.g., a reversible succinyl-CoA ligase), or a CoA transferase (e.g., a glutaconate CoA-transferase) and produce pimelic acid. For example, a recombinant host producing pimeloyl-CoA further can include an acetylating aldehyde dehydrogenase and produce pimelate semialdehyde. For example, a recombinant host producing pimelate further can include a carboxylate reductase and produce pimelate semialdehyde.

[0086] A recombinant hosts producing pimelic acid or pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a .omega.-transaminase and produce 7-aminoheptanoate. In some embodiments, a recombinant host producing pimelate includes a carboxylate reductase and a .omega.-transaminase to produce 7-aminoheptanoate.

[0087] A recombinant host producing pimelate or pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase or a 4-hydroxybutyrate dehydrogenase, and produce 7-hydroxyheptanoic acid. In some embodiments, a recombinant host producing pimeloyl-CoA includes an acetylating aldehyde dehydrogenase, and a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase or a 4-hydroxybutyrate dehydrogenase to produce 7-hydroxyheptanoate. In some embodiments, a recombinant host producing pimelate includes a carboxylate reductase and a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase or a 4-hydroxybutyrate dehydrogenase to produce 7-hydroxyheptanoate.

[0088] A recombinant hosts producing 7-aminoheptanoate, 7-hydroxyheptanoate or pimelate semialdehyde further can include at least one exogenous nucleic acid encoding a .omega.-transaminase, a deacetylase, a N-acetyl transferase, or an alcohol dehydrogenase, and produce heptamethylenediamine. For example, a recombinant host producing 7-hydroxyheptanoate can include a carboxylate reductase with a phosphopantetheine transferase enhancer, a .omega.-transaminase and an alcohol dehydrogenase.

[0089] A recombinant host producing 7-hydroxyheptanoic acid further can include one or more of a carboxylate reductase with a phosphopantetheine transferase enhancer and an alcohol dehydrogenase, and produce 1,7-heptanediol.

[0090] Within an engineered pathway, the enzymes can be from a single source, i.e., from one species or genus, or can be from multiple sources, i.e., different species or genera. Nucleic acids encoding the enzymes described herein have been identified from various organisms and are readily available in publicly available databases such as GenBank or EMBL.

[0091] Any of the enzymes described herein that can be used for production of one or more C7 building blocks can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of the corresponding wild-type enzyme. It will be appreciated that the sequence identity can be determined on the basis of the mature enzyme (e.g., with any signal sequence removed) or on the basis of the immature enzyme (e.g., with any signal sequence included). It also will be appreciated that the initial methionine residue may or may not be present on any of the enzyme sequences described herein.

[0092] For example, a polypeptide having fatty acid O-methyltransferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see GenBank Accession No. ACC41782.1, SEQ ID NO: 1), a Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 2), or a Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 3) methyltransferase. See, FIG. 9.

[0093] For example, a polypeptide having thioesterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO: 4) or a Lactobacillus plantarum (GenBank Accession No. CCC78182.1, SEQ ID NO: 5) acyl-[acp]thioesterase. See, FIG. 9.

[0094] For example, a polypeptide having pimelyl-[acp]methyl ester esterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichia coli pimelyl-[acp]methyl ester esterase (see GenBank Accession No. AAC76437.1, SEQ ID NO: 6). See, FIG. 9.

[0095] For example, a polypeptide having carboxylate reductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 7), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 8), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1, SEQ ID NO: 9), a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 10), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 11), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 12) carboxylate reductase. See, FIG. 9.

[0096] For example, a polypeptide having .omega.-transaminase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 14), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 17), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18) .omega.-transaminase. Some of these .omega.-transaminases are diamine .omega.-transaminases.

[0097] For example, a polypeptide having phosphopantetheinyl transferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Bacillus subtilis phosphopantetheinyl transferase (see Genbank Accession No. CAA44858.1, SEQ ID NO: 19) or a Nocardia sp. NRRL 5646 phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1, SEQ ID NO: 20). See, FIG. 9.

[0098] For example, a polypeptide having thioesterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichia coli thioesterase encoded by tesB (see GenBank Accession No. AAA24665.1, SEQ ID NO: 21). See, FIG. 9.

[0099] For example, a polypeptide having long-chain-fatty-acid-CoA ligase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichia coli long-chain-fatty-acid-CoA ligase (see Genbank Accession No. CAA50321.1, SEQ ID NO: 22), or a Cupriavidus necator long-chain-fatty-acid-CoA ligase (see Genbank Accession No. CAJ95550.1, SEQ ID NO: 23).

[0100] For example, a polypeptide having glutaconate CoA-transferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Acidaminococcus fermentans glutaconate CoA-transferase (see, e.g., Genbank Accession No. CAA57199.1 (GctA) and CAA57200.1 (GctB), SEQ ID NOs: 24 and 25, respectively).

[0101] For example, a polypeptide having enoyl-CoA reductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Treponema denticola enoyl-CoA reductase (see, e.g., Genbank Accession No. AAS11092.1, SEQ ID NO: 26) or to the amino acid sequence of an Euglena gracilis enoyl-CoA reductase (see, e.g., Genbank Accession No. AAW66853.1, SEQ ID NO: 27).

[0102] For example, a polypeptide having enoyl-CoA reductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Pseudomonas reinekei MT1 .beta.-ketothiolase (see, e.g., Genbank Accession No. ACZ63623.1, SEQ ID NO: 28), a Pseudomonas putida .beta.-ketothiolase (see, e.g., Genbank Accession No. AAA85138.1, SEQ ID NO: 29), a Burkholderia xenovorans .beta.-ketothiolase (see, e.g., Genbank Accession No. ABE33819.1, SEQ ID NO: 30), an Arthrobacter sp. .beta.-ketothiolase (see, e.g., Genbank Accession No. ABK03524.1, SEQ ID NO: 31), a Burkholderia xenovorans .beta.-ketothiolase (see, e.g., Genbank Accession No. ABE36495.1, SEQ ID NO: 32), a Geobacillus kaustophilus .beta.-ketothiolase (see, e.g., Genbank Accession No. BAD75605.1, SEQ ID NO: 33), a Gordonia bronchialis .beta.-ketothiolase (see, e.g., Genbank Accession ACY20886.1, SEQ ID NO: 34), a Citrobacter freundii .beta.-ketothiolase (see, e.g., Genbank Accession KFB98168.1, SEQ ID NO: 35), a Burkholderia sp. .beta.-ketothiolase (see, e.g., Genbank Accession ADG18081.1, SEQ ID NO: 36), a Beijerinckia indica .beta.-ketothiolase (see, e.g., Genbank Accession ACB95386.1, SEQ ID NO: 37), an Arthrobacter arilaitensis .beta.-ketothiolase (see, e.g., Genbank Accession CBT74677.1, SEQ ID NO: 38), a Cupriavidus necator .beta.-ketothiolase (see, e.g., Genbank Accession AAC38322.1, SEQ ID NO: 39), and an Escherichia coli .beta.-ketothiolase (see, e.g., Genbank Accession AAC74479.1, SEQ ID NO: 40).

[0103] The percent identity (homology) between two amino acid sequences can be determined as follows. First, the amino acid sequences are aligned using the BLAST 2 Sequences (Bl2seq) program from the stand-alone version of BLASTZ containing BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (e.g., www.fr.com/blast/) or the U.S. government's National Center for Biotechnology Information web site (www.ncbi.nlm.nih.gov). Instructions explaining how to use the Bl2seq program can be found in the readme file accompanying BLASTZ. Bl2seq performs a comparison between two amino acid sequences using the BLASTP algorithm. To compare two amino acid sequences, the options of Bl2seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., C:\seq1.txt); -j is set to a file containing the second amino acid sequence to be compared (e.g., C:\seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., C:\output.txt); and all other options are left at their default setting. For example, the following command can be used to generate an output file containing a comparison between two amino acid sequences: C:\Bl2seq -i c:\seq1.txt -j c:\seq2.txt -p blastp -o c:\output.txt. If the two compared sequences share homology (identity), then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology (identity), then the designated output file will not present aligned sequences. Similar procedures can be following for nucleic acid sequences except that blastn is used.

[0104] Once aligned, the number of matches is determined by counting the number of positions where an identical amino acid residue is presented in both sequences. The percent identity (homology) is determined by dividing the number of matches by the length of the full-length polypeptide amino acid sequence followed by multiplying the resulting value by 100. It is noted that the percent identity (homology) value is rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 is rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded up to 78.2. It also is noted that the length value will always be an integer.

[0105] It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given enzyme can be modified such that optimal expression in a particular species (e.g., bacteria or fungus) is obtained, using appropriate codon bias tables for that species.

[0106] Functional fragments of any of the enzymes described herein can also be used in the methods of the document. The term "functional fragment" as used herein refers to a peptide fragment of a protein that has at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 91%; 92%; 93%; 94%; 95%; 96%; 97%; 98%; 99%; 100%; or even greater than 100%) of the activity of the corresponding mature, full-length, wild-type protein. The functional fragment can generally, but not always, be comprised of a continuous region of the protein, wherein the region has functional activity. Functional fragments are shorter than corresponding mature proteins but are generally at least 25 (e.g., at least: 30; 40; 50; 60; 70; 80, 90; 100; 120; 150; 200; 250; 300; 450; 500; 800; or more) amino acids long.

[0107] This document also provides (i) functional variants of the enzymes used in the methods of the document and (ii) functional variants of the functional fragments described above. Functional variants of the enzymes and functional fragments can contain additions, deletions, or substitutions relative to the corresponding wild-type sequences. Enzymes with substitutions will generally have not more than 50 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, or 50) amino acid substitutions (e.g., conservative substitutions). This applies to any of the enzymes described herein and functional fragments. A conservative substitution is a substitution of one amino acid for another with similar characteristics. Conservative substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine. The nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a nonconservative substitution is a substitution of one amino acid for another with dissimilar characteristics.

[0108] Deletion variants can lack one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid segments (of two or more amino acids) or non-contiguous single amino acids. Additions (addition variants) include fusion proteins containing: (a) any of the enzymes described herein or a fragment thereof; and (b) internal or terminal (C or N) irrelevant or heterologous amino acid sequences. In the context of such fusion proteins, the term "heterologous amino acid sequences" refers to an amino acid sequence other than (a). A heterologous sequence can be, for example a sequence used for purification of the recombinant protein (e.g., FLAG, polyhistidine (e.g., hexahistidine), hemagglutinin (HA), glutathione-S-transferase (GST), or maltose binding protein (MBP)). Heterologous sequences also can be proteins useful as detectable markers, for example, luciferase, green fluorescent protein (GFP), or chloramphenicol acetyl transferase (CAT). In some embodiments, the fusion protein contains a signal sequence from another protein. In certain host cells (e.g., yeast host cells), expression and/or secretion of the target protein can be increased through use of a heterologous signal sequence. In some embodiments, the fusion protein can contain a carrier (e.g., KLH) useful, e.g., in eliciting an immune response for antibody generation) or ER or Golgi apparatus retention signals. Heterologous sequences can be of varying length and in some cases can be a longer sequences than the full-length target proteins to which the heterologous sequences are attached.

[0109] Engineered hosts can naturally express none or some (e.g., one or more, two or more, three or more, four or more, five or more, or six or more) of the enzymes of the pathways described herein. Thus, a pathway within an engineered host can include all exogenous enzymes, or can include both endogenous and exogenous enzymes. Endogenous genes of the engineered hosts also can be disrupted to prevent the formation of undesirable metabolites or prevent the loss of intermediates in the pathway through other enzymes acting on such intermediates. Engineered hosts can be referred to as recombinant hosts or recombinant host cells. As described herein recombinant hosts can include nucleic acids encoding one or more of a methyltransferase, an esterase, a synthase, a dehydratase, a hydratase, a dehydrogenase, a thioesterase, a reversible CoA-ligase, a CoA-transferase, a reductase, deacetylase, N-acetyl transferase or a .omega.-transaminase as described in more detail below.

[0110] In addition, the production of one or more C7 building blocks can be performed in vitro using the isolated enzymes described herein, using a lysate (e.g., a cell lysate) from a host microorganism as a source of the enzymes, or using a plurality of lysates from different host microorganisms as the source of the enzymes.

Biosynthetic Methods

[0111] The present document provides methods of shielding a carbon chain aliphatic backbone, functionalized with terminal carboxyl groups, in a recombinant host. The method can include enzymatically converting a n-carboxy-2-enoic acid to a n-carboxy-2-enoate methyl ester in the host using a polypeptide having the activity of a fatty acid O-methyltransferase, wherein n+1 reflects length of the carbon chain aliphatic backbone. For example, the n-carboxy-2-enoic acid can be four to 18, four to 16, four to 14, four to 12, four to 10, five to 10, five to nine, or five to eight carbons in length such as 2(E)-heptenedioic acid, and can be enzymatically converted to the corresponding methyl ester, e.g., 2(E)-heptenedioate methyl ester, The polypeptide having fatty acid O-methyltransferase activity can be classified under EC 2.1.1.15. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.

[0112] In some embodiments, the method further includes enzymatically converting 2(E)-heptenedioate methyl ester to pimeloyl-CoA. For example, the method further can include enzymatically converting pimeloyl-CoA to a product selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol, for example, using one or more polypeptides having thioesterase, reversible CoA-ligase, glutaconate CoA-transferase, .omega.-transaminase, 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, alcohol dehydrogenase, carboxylate reductase or alcohol dehydrogenase activity.

[0113] The present document further provides methods of producing 2(E)-heptenedioyl-CoA methyl ester in a recombinant host. The method can include enzymatically converting 2(E)-heptenedioate to 2(E)-heptenedioate methyl ester in the recombinant host using a polypeptide having fatty acid O-methyltransferase activity. The polypeptide having fatty acid O-methyltransferase activity can be classified under EC 2.1.1.15. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. The method further can include enzymatically converting 2(E)-heptenedioate methyl ester to pimeloyl-CoA methyl ester.

[0114] In some embodiments, 2(E)-heptenedioate is enzymatically produced from 2(E)-heptenedioyl-CoA. For example, a polypeptide having thioesterase or CoA-transferase activity can enzymatically convert 2(E)-heptenedioyl-CoA to 2(E)-heptenedioate. In some embodiments, the polypeptide having thioesterase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 4 or SEQ ID NO: 5. In some embodiments, the polypeptide having CoA-transferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24 or SEQ ID NO: 25.

[0115] In some embodiments, 2(E)-heptenedioate methyl ester is enzymatically converted to 2(E)-heptenedioyl-CoA methyl ester using a polypeptide having CoA ligase activity classified under EC 6.2.1.-, e.g., EC 6.2.1.2 or EC 6.2.1.3.

[0116] In some embodiments, the method further includes enzymatically converting 2(E)-heptenedioyl-CoA methyl ester to pimeloyl-CoA methyl ester. In some embodiments, a polypeptide having trans-2-enoyl-CoA reductase activity enzymatically converts 2(E)-heptenedioyl-CoA methyl ester to pimeloyl-CoA methyl ester.

[0117] In some embodiments, the method further includes enzymatically converting pimeloyl-CoA methyl ester to pimeloyl-CoA. In some embodiments, a polypeptide having pimelyl-[acp]methyl ester esterase activity enzymatically converts pimeloyl-CoA methyl ester to pimeloyl-CoA. In some embodiments, the polypeptide having pimelyl-[acp]methyl ester esterase activity has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 6.

[0118] In some embodiments, the method further includes enzymatically converting pimeloyl-CoA to a product selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol. In some embodiments, the method comprises enzymatically converting pimeloyl-CoA to pimelic acid using a polypeptide having thioesterase, reversible CoA-ligase, or glutaconate CoA-transferase activity.

[0119] In some embodiments, the method further includes enzymatically converting pimelic acid to pimelate semialdehyde using a polypeptide having carboxylate reductase activity. In some embodiments, the polypeptide having carboxylate reductase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NOs: 7 to 12.

[0120] In some embodiments, the method includes enzymatically converting pimeloyl-CoA to pimelate semialdehyde using a polypeptide having acetylating aldehyde dehydrogenase activity. In some embodiments, the method further includes enzymatically converting pimelate semialdehyde to pimelic acid using a polypeptide having 5-oxopentanoate dehydrogenase, 6-oxohexanoate dehydrogenase, 7-oxoheptanoate dehydrogenase, or aldehyde dehydrogenase activity.

[0121] In some embodiments, the method further includes enzymatically converting pimelate semialdehyde to 7-aminoheptanoate using a polypeptide having .omega.-transaminase activity. In some embodiments, the polypeptide having .omega.-transaminase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NOs: 13 to 18.

[0122] In some embodiments, the method further includes enzymatically converting pimelate semialdehyde to heptamethylenediamine using a polypeptide having co-transaminase activity.

[0123] In some embodiments, the method further includes enzymatically converting pimelate semialdehyde to 7-hydroxyheptanoate using a polypeptide having 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, or alcohol dehydrogenase activity.

[0124] In some embodiments, the method further includes enzymatically converting 7-hydroxyheptanoate to 1,7-heptanediol using a polypeptide having carboxylate reductase or alcohol dehydrogenase activity.

[0125] In some embodiments, one or more steps of the method are performed by fermentation. In some embodiments, the host is subjected to a cultivation strategy under aerobic, anaerobic, micro-aerobic, or mixed oxygen/denitrification cultivation conditions. In some embodiments, the host is cultured under conditions of phosphate, oxygen, and/or nitrogen limitation. In some embodiments, the host is retained using a ceramic membrane to maintain a high cell density during fermentation.

[0126] In some embodiments, the principal carbon source fed to the fermentation derives from biological or non-biological feedstocks. In some embodiments, the biological feedstock is, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid, formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste. In some embodiments, the non-biological feedstock is, or derives from, natural gas, syngas, CO.sub.2/H.sub.2, methanol, ethanol, benzoate, non-volatile residue (NVR) caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

[0127] In some embodiments, the host comprises one or more polypeptides having attenuated polyhydroxyalkanoate synthase, acetyl-CoA thioesterase, acetyl-CoA specific fl-ketothiolase, phosphotransacetylase forming acetate, acetate kinase, lactate dehydrogenase, menaquinol-fumarate oxidoreductase, 2-oxoacid decarboxylase producing isobutanol, alcohol dehydrogenase forming ethanol, triose phosphate isomerase, pyruvate decarboxylase, glucose-6-phosphate isomerase, transhydrogenase dissipating the NADPH imbalance, glutamate dehydrogenase dissipating the NADPH imbalance, NADH/NADPH-utilizing glutamate dehydrogenase, pimeloyl-CoA dehydrogenase; acyl-CoA dehydrogenase accepting C7 building blocks and central precursors as substrates; glutaryl-CoA dehydrogenase; or pimeloyl-CoA synthetase activity.

[0128] In some embodiments, the host overexpresses one or more genes encoding a polypeptide having acetyl-CoA synthetase; 6-phosphogluconate dehydrogenase; transketolase; puridine nucleotide transhydrogenase; formate dehydrogenase; glyceraldehyde-3P-dehydrogenase; malic enzyme; glucose-6-phosphate dehydrogenase; fructose 1,6 diphosphatase; L-alanine dehydrogenase; PEP carboxylase, pyruvate carboxylase; PEP carboxykinase; PEP synthase; L-glutamate dehydrogenase specific to the NADPH used to generate a co-factor imbalance; methanol dehydrogenase, formaldehyde dehydrogenase, lysine transporter; dicarboxylate transporter; S-adenosylmethionine synthetase; 3-phosphoglycerate dehydrogenase; 3-phosphoserine aminotransferase; phosphoserine phosphatase; or a multidrug transporter activity.

[0129] In some embodiments, the host is a prokaryote, e.g., Escherichia coli, Clostridium ljungdahlii, Clostridium autoethanogenum, Clostridium kluyveri, Corynebacterium glutamicum, Cupriavidus necator, Cupriavidus metallidurans, Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas oleavorans, Delftia acidovorans, Bacillus subtillis, Lactobacillus delbrueckii, Lactococcus lactis, and Rhodococcus equi.

[0130] In some embodiments, the host is a eukaryote, e.g., Aspergillus niger, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Issathenkia orientalis, Debaryomyces hansenii, Arxula adenoinivorans, and Kluyveromyces lactis.

Enzymes Converting 2(E)-Heptenedioyl-CoA to 2(E)-Heptenedioyl-CoA Methyl Ester

[0131] As depicted in FIGS. 1 to 3, a 2(E)-heptenedioate methyl ester can be formed from 2(E)-heptenedioate using a fatty acid O-methyltransferase, such as the fatty acid O-methyltransferase classified, for example, under EC 2.1.1.15. For example, the fatty acid O-methyltransferase can be obtained from Mycobacterium marinum M (GenBank Accession No. ACC41782.1. SEQ ID NO: 1); Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 2), or Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 3).

[0132] 2(E)-heptenedioate methyl ester can be converted to 2(E)-heptenedioyl-CoA methyl ester using, for example, a CoA ligase classified, for example, under EC 6.2.1.-. In some embodiments, a butyrate-CoA ligase classified under EC 6.2.1.2 or a long-chain-fatty-acid-CoA ligase classified under EC 6.2.1.3 such as the long chain fatty acid CoA-ligase from Escherichia coli (Genbank Accession No. CAA50321.1, SEQ ID NO: 22) or Cupriavidus necator (Genbank Accession No. CAJ95550.1, SEQ ID NO: 23) can be used to convert 2(E)-heptenedioate methyl ester to 2(E)-heptendioyl-CoA methyl ester. See, FIGS. 1 to 3.

[0133] In some embodiments, 2(E)-heptenedioate can be formed from 2(E)-heptenedioyl-CoA (also known as 2,3-dehydropimeloyl-CoA) using, for example, a thioesterase classified under EC 3.1.2.-, such as the acyl-[acp]thioesterase from Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO: 4) or from Lactobacillus plantarum (GenBank Accession No. CCC78182.1, SEQ ID NO: 5). Such acyl-[acp]thioesterases have C6-C8 chain length specificity (see, for example, Jing et al., 2011, BMC Biochemistry, 12(44)). See, e.g., FIG. 1.

[0134] In some embodiments, 2(E)-heptenedioate can be formed from 2(E)-heptenedioyl-CoA using, for example, a CoA-transferase (e.g., a glutaconate CoA-transferase) classified, for example, under EC 2.8.3.12 such as the gene product of GctAB from Acidaminococcus fermentans (Genbank Accession No. CAA57199.1 (GctA) & CAA57200.1 (GctB), SEQ ID NOs: 24 and 25, respectively). See, for example, Buckel et al., 1981, Eur. J. Biochem., 118:315-321. See, e.g., FIGS. 2 and 3.

Enzymes Producing 2(E)-Heptenedioyl-CoA from Glutaryl-CoA

[0135] As depicted in FIG. 1, glutaryl-CoA can be formed from the central metabolites 2-oxoglutarate or acetyl-CoA via carbon chain elongation (i) associated with lysine biosynthesis via .alpha.-aminoadipate or (ii) associated with cyclohexane carboxylate biosynthesis in Synthrophus aciditrophicus. Glutaryl-CoA can be converted to 2(E)-heptenedioyl-CoA using a (i) .beta.-ketoacyl-[acp]synthase or .beta.-ketothiolase, (ii) a 3-hydroxybutyryl-CoA dehydrogenase, and a (iii) an enoyl-CoA hydratase.

[0136] For example, glutaryl-CoA can be formed via C1 carbon chain elongation associated with lysine biosynthesis via .alpha.-aminoadipate, which comprises using (i) a homocitrate synthase, (ii) a homocitrate dehydratase and a homoaconitate hydratase, (iii) an isohomocitrate dehydrogenase, (iv) an decarboxylase such as an indolepyruvate decarboxylase, (vi) a glutarate-semialdehyde dehydrogenase and (v) a glutarate:CoA ligase. See, e.g., FIG. 1.

[0137] For example, glutaryl-CoA can be formed via CoA-dependent carbon chain elongation associated with cyclohexane carboxylate biosynthesis in Synthrophus aciditrophicus which comprises using (i) a .beta.-ketothiolase or an acetyl-carboxylase in combination with an acetoacetyl-CoA synthase, (ii) a 3-hydroxybutyryl-CoA dehydrogenase, (iii) an enoyl-CoA hydratase, and either (iv) a glutaryl-CoA dehydrogenase in combination with an enoyl-CoA reductase or a trans-2-enoyl-CoA reductase or (v) a glutaconyl-CoA decarboxylase. See, e.g., FIG. 1.

[0138] In some embodiments, a (homo).sub.ncitrate synthase can be classified, for example, under EC 2.3.3.14 or EC 2.3.3.13, such as the gene product of aksA from Methanocaldococcus jannaschii (see Genbank Accession No. AAB98494.1).

[0139] In some embodiments, the combination of (homo).sub.ncitrate dehydratase and (homo).sub.naconitate hydratase can be classified, for example, under EC 4.2.1.- (e.g., EC 4.2.1.114, EC 4.2.1.36 or EC 4.2.1.33), such as the gene product of aksD from Methanocaldococcus jannaschii (see, Genbank Accession No. AAB990070.1) or gene product of aksE from Methanocaldococcus jannaschii (see, Genbank Accession No. AAB99277.1). The gene products of aksD and aksE are subunits of an enzyme classified under EC 4.2.1.114. The gene products of LeuC and LeuD are subunits of an enzyme classified under EC 4.2.1.33.

[0140] In some embodiments, an iso(homo).sub.ncitrate dehydrogenase can be classified, for example, under EC 1.1.1.- such as EC 1.1.1.85, EC 1.1.1.87 or EC 1.1.1.286, such as the gene product of aksF from Methanocaldococcus jannaschii (see, Genbank Accession No. ACA28837.1), the gene product of LYS12 from Saccharomyces cerevisiae (See Genbank Accession No. CAA86700.1) or hicdh from Thermus thermophiles (see Genbank Accession No. BAB88861.1).

[0141] In some embodiments, 2-oxo-adipate can be decarboxylated by a decarboxylase classified, for example, under EC 4.1.1.43, EC 4.1.1.72, or EC 4.1.1.74 such as the indole-3-pyruvate decarboxylase from Salmonella typhimurium (see, for example, Genbank Accession No. CAC48239.1). A mutant variant of the indolepyruvate decarboxylase from Salmonella typhimurium was engineered successfully to selectively accept longer chain length substrates. The L544A mutation of the sequence provided in Genbank Accession No. CAC48239.1 allowed for 567 times higher selectivity towards the C7 2-oxoacid than towards the C5 2-oxoacid (see, Xiong et al., 2012, Scientific Reports, 2: 311). The 2-oxoglutarate dehydrogenase complex has demonstrated activity for 2-oxoglutarate and 2-oxoadipate (Bunik et al., 2000, Eur. J. Biochem., 267, 3583-3591).

[0142] 2-oxo-adipate also can be decarboxylated by a 2-oxoglutarate dehydrogenase complex comprised of enzymes homologous to enzymes classified, for example, under EC 1.2.4.2, EC 1.8.1.4, and EC 2.3.1.61. The 2-oxoglutarate dehydrogenase complex contains multiple copies of a 2-oxoglutarate dehydrogenase classified, for example, under EC 1.2.4.2 bound to a core of dihydrolipoyllysine-residue succinyltransferases classified, for example, under EC 2.3.1.61, which also binds multiple copies of a dihydrolipoyl dehydrogenase classified, for example, under EC 1.8.1.4.

[0143] In some embodiments, a 5-oxopentanoate dehydrogenase (e.g., a glutarate semialdehyde dehydrogenase) can be classified, for example under EC 1.2.1.- (e.g., EC 1.2.1.20, EC 1.2.1.16 or EC 1.2.1.79) such as the gene product of CpnE (see, for example, Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684).

[0144] In some embodiments, a glutarate CoA ligase can be classified, for example, under EC 6.2.1.6.

[0145] In some embodiments, a .beta.-ketothiolase can be classified under EC 2.3.1.- (e.g., EC 2.3.1.9, EC 2.3.1.16, or EC 2.3.174). For example, a .beta.-ketothiolase can be classified under EC 2.3.1.9, such as the gene product of atoB or phaA. The .beta.-ketothiolase encoded by atoB or phaA accepts acetyl-CoA as substrates, forming acetoacetyl-CoA (see, Haywood et al., 1988, supra; Slater et al., 1998, supra). The .beta.-ketothiolase encoded by paaJ (see, e.g., Genbank Accession No. AAC74479.1), catF and pcaF can be classified under, for example, EC 2.3.1.174. The .beta.-ketothiolase encoded by paaJ condenses acetyl-CoA and succinyl-CoA to 3-oxoadipyl-CoA (see, for example, Fuchs et al., 2011, Nature Reviews Microbiology, 9, 803-816; Gobel et al., 2002, J. Bacteriol., 184(1), 216-223). A homologue of paaJ in Synthrophus aciditrophicus catalyses the condensation of acetyl-CoA and glutaryl-CoA to 3-oxopimeloyl-CoA such as Genbank Accession No. ABC78517.1 or Genbank Accession No. ABC78881.1. Alternately, a .beta.-ketoacyl-[acp]homologue of paaJ in S. aciditrophicus catalyses the condensation of acetyl-CoA and glutaryl-CoA to 3-oxopimeloyl-CoA.

[0146] An acetyl-CoA carboxylase can be classified under EC 6.4.1.2 and an acetoacetyl-CoA synthase can be classified under EC 2.3.1.194. Conversion of acetyl-CoA to malonyl-CoA by an acetyl-CoA carboxylase has been shown to increase the rate of fatty acid synthesis (Davis et al., J. Biol. Chem., 2000, 275(37), 28593-28598). It has been demonstrated that acetoacetyl-CoA synthase may be used as an irreversible substitute for the gene product of phaA in the carbon chain elongation associated with polyhydroxybutyrate synthesis (Matsumoto et al., Biosci. Biotechnol. Biochem., 2011, 75(2), 364-366).

[0147] In some embodiments, a 3-hydroxybutyryl-CoA dehydrogenase (also can be referred to as a 3-hydroxyacyl-CoA dehydrogenase) can be classified under EC 1.1.1.157 such as the gene product hbd (see, for example, Shen et al., Appl. Environ. Microbiol., 2011, 77(9), 2905-2915; Budde et al., J. Bacteriol., 2010, 192(20), 5319-5328) or the gene product of paaH (Teufel et al., 2010, Proc. Natl. Acad. Sci. 107(32), 14390-14395).

[0148] In some embodiments, an enoyl-CoA hydratase can be classified under EC 4.2.1.17, such as the gene product of crt (see, for example, Shen et al., 2011, supra; Fukui et al., J. Bacteriol., 1998, 180(3), 667-673) or the gene product of paaF (see, for example, Fuchs et al., 2011, supra). Homologs of paaF in S. aciditrophicus include the enoyl-CoA hydratase of Genbank Accession No. ABC77794.1 or the enoyl-CoA dehydratase of Genbank Accession No. ABC78950.1.

[0149] In some embodiments, a reversible glutaconyl-CoA decarboxylase that relies on a Na.sup.+ membrane pump can be classified, for example, under EC 4.1.1.70 (see Mouttaki et al., Appl. Environ. Microbiol., 2007, 73(3), 930-938). The EC 4.1.1.70 enzyme activity is associated with the following subunits in S. aciditrophicus, viz. Genbank Accession Nos. (1) ABC77900.1, (2) ABC76114.1 and (3) ABC77898.1.

[0150] In some embodiments, an enoyl-[acp]reductase can be classified under EC 1.3.1.- (e.g., EC 1.3.1.9) such as the enoyl-[acp]reductase obtained from S. aciditrophicus or the gene product of FabI (Genbank Accession No: CAB13029.2) from Bacillus subtillis (see, for example, Heath et al., 2000, J. Biol. Chem., 275(51), 40128-33). The enoyl-[acp]reductase involved in fatty acid synthesis in S. aciditrophicus likely accepts CoA activated dicarboxylic acids (Mouttaki et al., 2007, supra).

[0151] In some embodiments, a trans-2-enoyl-CoA reductase can be classified, for example, under EC 1.3.1.44, such as the gene product of ter (Genbank Accession No. AAW66853.1) (Hoffmeister et al., 2005, J. Biol. Chem., 280(6), 4329-4338; Shen et al., 2011, supra) or tdter (Genbank Accession No. AAS11092.1) (Bond-Watts et al., Biochemistry, 2012, 51, 6827-6837).

[0152] A .beta.-ketoacyl-[acp]synthase can be classified, for example, under, EC 2.3.1.41, EC 2.3.1.179, or EC 2.3.1.180. The .beta.-ketothiolases and .beta.-ketoacyl-[acp]synthases involved in fatty acid synthesis in S. aciditrophicus likely accept CoA activated dicarboxylic acids (Mouttaki et al., Appl. Environ. Microbiol., 2007, 73(3), 930-938).

Enzymes Producing 2(E)-Heptenedioyl-CoA from 2-Oxo-Pimelate

[0153] As depicted in FIG. 2, 2-oxo-pimelate can be formed from the central metabolite 2-oxoglutarate via two rounds of carbon chain elongation associated with lysine biosynthesis via .alpha.-aminoadipate, where each round of elongation comprises using (i) a homocitrate synthase, (ii) a homocitrate dehydratase and a homoaconitate hydratase, and (iii) an isohomocitrate dehydrogenase. The homocitrate synthase, a homocitrate dehydratase, homoaconitate hydratase, and isohomocitrate dehydrogenase are described above. 2-oxo-pimelate also can be formed from succinate semialdehyde using a 4-hydroxy-2-oxoheptanedioate aldolase, a 2-oxo-hept-3-ene-1,7-dioate hydratase, and a 2-enoate reductase as shown in FIG. 3.

[0154] 2-oxo-pimelate can be converted to 2(E)-heptenedioyl-CoA using (i) a 2-hydroxyglutarate dehydrogenase or (ii) a lactate dehydrogenase, (ii) a CoA-transferase such as a glutaconate CoA-transferase, and (iii) a 2-hydroxyglutaryl-CoA dehydratase or a 2-hydroxyisocaproyl-CoA dehydratase. See, FIGS. 2 and 3.

[0155] A 2-hydroxyglutarate dehydrogenase can be classified, for example under EC 1.1.1.-(337) such as the gene product of HgdH or ldhA. See, Djurdjevic et al, 2011, Appl. Environ. Microbiol., 77(1), 320-322 and Kim et al., 2005, FEBS Journal, 272, 550-561.

[0156] A CoA-transferase such as a glutaconate CoA-transferase can be classified, for example, under EC 2.8.3.12 and can be obtained from Acidaminococcus fermentans (see, e.g., SEQ ID NOs: 24 and 25). See, for example, Buckel et al., 1981, Eur. J. Biochem., 118:315-321.

[0157] A 2-hydroxyglutaryl-CoA dehydratase can be classified, for example, under EC 4.2.1.- such as the gene product of HgdAB (Genbank Accession Nos. AAD31677.1 and AAD31675.1) in combination with an activator, the gene product of HgdC (Genbank Accession No. CAA42196.1). The HgdAB gene product contains subunits A and B. See, Djurdjevic et al, 2011, supra. A 2-hydroxyisocaproyl-CoA dehydratase can be classified, for example, under EC 4.2.1.- such as the gene product of hadBC (Genbank Accession Nos. AAV40819.1 & AAV40820.1) or hadI (Genbank Accession No. AAV40818.1).

[0158] A 4-hydroxy-2-oxoheptanedioate aldolase can be classified, for example, under EC 4.1.2.52 such as the gene product of HpaI. See Genbank Accession No. CAA87759.1.

[0159] A 2-oxo-hept-3-ene-1,7-dioate hydratase can be classified, for example, under EC 4.2.1.- such as the gene product of HpaH. See GenBank Accession No. AAB91474.1.

[0160] In some embodiments, a 2-enoate reductase may be classified under EC 1.3.1.- such as EC 1.3.1.31 or EC 1.6.99.1 such as originating from Bacillus subtilis (Genbank Accession No. BAA12619.1), Pseudomonas putida Genbank Accession No. AAN66878.1), Kluyveromyces lactis (Genbank Accession No. AAA98815.1), Lactobacillus casei (Genbank Accession No. AGP69310.1), Saccharomyces pastorianus (Genbank Accession No. CAA37666.1), Thermoanaerobacter pseudethanolicus (Genbank Accession No. ABY93685.1), or Enterobacter cloacae (Genbank Accession No. AAB38683.1) (Gao et al., 2012, Enzyme Microb. Technol., 51(1), 26-34).

Enzymes Facilitating Introduction of Terminal Functional Groups in the Biosynthesis of a C7 Building Block

[0161] In some embodiments, a carboxylate reductase facilitates the generation of a terminal aldehyde group for subsequent conversion to an amine group by an .omega.-transaminase or to a hydroxyl group by an alcohol dehydrogenase. The carboxylate reductase can be obtained, for example, from Mycobacterium marinum (Genbank Accession No. ACC40567.1, SEQ ID NO: 7), Mycobacterium smegmatis (Genbank Accession No. ABK71854.1, SEQ ID NO: 8), Segniliparus rugosus (Genbank Accession No. EFV11917.1, SEQ ID NO: 9), Mycobacterium smegmatis (Genbank Accession No. ABK75684.1, SEQ ID NO: 10), Mycobacterium massiliense (Genbank Accession No. EIV11143.1, SEQ ID NO: 11), or Segniliparus rotundus (Genbank Accession No. ADG98140.1, SEQ ID NO: 12). See, e.g., FIGS. 4 to 8.

[0162] The carboxylate reductase encoded by the gene product of car and enhancer npt has broad substrate specificity, including terminal difunctional C4 and C5 carboxylic acids (Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42, 130-137).

Enzymes Generating the Terminal Carboxyl Groups in the Biosynthesis of C7 Building Blocks

[0163] As depicted in FIG. 4, a terminal carboxyl group can be enzymatically formed using a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a CoA-transferase or a reversible CoA-ligase.

[0164] In some embodiments, the first terminal carboxyl group leading to the synthesis of a C7 building block is enzymatically formed by a pimelyl-[acp]methyl ester esterase classified, for example, under EC 3.1.1.85 such as the gene product of bioH (GenBank Accession No. AAC76437.1, SEQ ID NO: 6). See, FIGS. 1 and 2.

[0165] In some embodiments, the second terminal carboxyl group leading to the synthesis of a C7 building block is enzymatically formed by a thioesterase classified under EC 3.1.2.-, such as the gene product of YciA, tesB (Genbank Accession No. AAA24665.1, SEQ ID NO: 21), Acot13 or originating from Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO: 4) or from Lactobacillus plantarum (GenBank Accession No. CCC78182.1, SEQ ID NO: 5) (see, for example, Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang et al., Biochemistry, 2008, 47(9), 2789-2796; Naggert et al., J. Biol. Chem., 1991, 266(17), 11044-11050; or Jing et al., 2011, BMC Biochemistry, 12(44)).

[0166] In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by an aldehyde dehydrogenase classified, for example, under EC 1.2.1.3 (see, for example, Guerrillot & Vandecasteele, Eur. J. Biochem., 1977, 81, 185-192).

[0167] In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a dehydrogenase classified under EC 1.2.1.- (e.g., EC 1.2.1.16, EC 1.2.1.20, EC 1.2.1.79, EC 1.2.1.3 or EC 1.2.1.63) such as 5-oxopentanoate dehydrogenase (e.g., the gene product of CpnE from Comamonas sp.), 6-oxohexanoate dehydrogenase (e.g., the gene product of ChnE from Acinetobacter sp.) or a 7-oxoheptanoate dehydrogenase (e.g., the gene product of ThnG from Sphingomonas macrogolitabida). See, for example, Iwaki et al., Appl. Environ. Microbiol., 1999, 65(11), 5158-5162; Iwaki et al., Appl. Environ. Microbiol., 2002, 68(11), 5671-5684; or Lopez-Sanchez et al., Appl. Environ. Microbiol., 2010, 76(1), 110-118. For example, a 6-oxohexanoate dehydrogenase can be classified under EC 1.2.1.63. For example, a 7-oxoheptanoate dehydrogenase can be classified under EC 1.2.1.-.

[0168] In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 such as from Acidaminococcus fermentans. See, for example, Buckel et al., 1981, Eur. J. Biochem., 118:315-321.

[0169] In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid is enzymatically formed by a reversible CoA-ligase such as a succinate-CoA ligase classified, for example, under EC 6.2.1.5 such as from Thermococcus kodakaraensis. See, for example, Shikata et al., 2007, J. Biol. Chem., 282(37):26963-26970.

Enzymes Generating the Terminal Amine Groups in the Biosynthesis of C7 Building Blocks

[0170] As depicted in FIGS. 5 and 6, terminal amine groups can be enzymatically formed using a .omega.-transaminase or a deacetylase.

[0171] In some embodiments, the first or second terminal amine group leading to the synthesis of 7-aminoheptanoic acid is enzymatically formed by a .omega.-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as that obtained from Chromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), Pseudomonas aeruginosa (Genbank Accession No. AAG08191.1, SEQ ID NO: 14), Pseudomonas syringae (Genbank Accession No. AAY39893.1, SEQ ID NO: 15), Rhodobacter sphaeroides (Genbank Accession No. ABA81135.1, SEQ ID NO: 16), Escherichia coli (Genbank Accession No. AAA57874.1, SEQ ID NO: 17), Vibrio fluvialis (Genbank Accession No. AEA39183.1, SEQ ID NO: 18), Streptomyces griseus, or Clostridium viride. Some of these .omega.-transaminases are diamine .omega.-transaminases (e.g., SEQ ID NO: 17). For example, the .omega.-transaminases classified, for example, under EC 2.6.1.29 or EC 2.6.1.82 may be diamine .omega.-transaminases.

[0172] The reversible .omega.-transaminase from Chromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO: 13) has demonstrated analogous activity accepting 6-aminohexanoic acid as amino donor, thus forming the first terminal amine group in adipate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).

[0173] The reversible 4-aminobubyrate:2-oxoglutarate transaminase from Streptomyces griseus has demonstrated analogous activity for the conversion of 6-aminohexanoate to adipate semialdehyde (Yonaha et al., Eur. J. Biochem., 1985, 146:101-106).

[0174] The reversible 5-aminovalerate transaminase from Clostridium viride has demonstrated analogous activity for the conversion of 6-aminohexanoate to adipate semialdehyde (Barker et al., J. Biol. Chem., 1987, 262(19), 8994-9003).

[0175] In some embodiments, a terminal amine group leading to the synthesis of 7-aminoheptanoate or heptamethylenediamine is enzymatically formed by a diamine .omega.-transaminase. For example, the second terminal amino group can be enzymatically formed by a diamine .omega.-transaminase classified, for example, under EC 2.6.1.29 or classified, for example, under EC 2.6.1.82, such as the gene product of YgjG from E. coli (Genbank Accession No. AAA57874.1, SEQ ID NO: 17).

[0176] The gene product of ygjG accepts a broad range of diamine carbon chain length substrates, such as putrescine, cadaverine and spermidine (see, for example, Samsonova et al., BMC Microbiology, 2003, 3:2).

[0177] The diamine .omega.-transaminase from E. coli strain B has demonstrated activity for 1,7 diaminoheptane (Kim, The Journal of Chemistry, 1964, 239(3), 783-786).

[0178] In some embodiments, the second terminal amine group leading to the synthesis of heptamethylenediamine is enzymatically formed by a deacetylase such as an acyl-lysine deacylase classified, for example, under EC 3.5.1.17 or such as acetylputrescine deacetylase classified, for example, under EC 3.5.1.62. The acetylputrescine deacetylase from Micrococcus luteus K-11 accepts a broad range of carbon chain length substrates, such as acetylputrescine, acetylcadaverine and N.sup.8-acetylspermidine (see, for example, Suzuki et al., 1986, BBA--General Subjects, 882(1):140-142).

Enzymes Generating the Terminal Hydroxyl Groups in the Biosynthesis of C7 Building Blocks

[0179] As depicted in FIGS. 7 and 8, a terminal hydroxyl group can be enzymatically formed using 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, or an alcohol dehydrogenase.

[0180] For example, a terminal hydroxyl group leading to the synthesis of 7-hydroxyheptanoic acid can be enzymatically formed by a dehydrogenase classified, for example, under EC 1.1.1.- such as a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258 (e.g., the gene from of ChnD), a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.- such as the gene product of CpnD (see, for example, Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684), a 5-hydroxypentanoate dehydrogenase from Clostridium viride, or a 4-hydroxybutyrate dehydrogenase such as gabD (see, for example, Lutke-Eversloh & Steinbuchel, 1999, FEMS Microbiology Letters, 181(1):63-71). See, FIG. 7.

[0181] In some embodiments, the second terminal hydroxyl group leading to the synthesis of 1,7 heptanediol is enzymatically formed by an alcohol dehydrogenase classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184).

Biochemical Pathways

Pathway Using Acetyl-CoA or 2-Oxo-Glutarate as Central Metabolite in the Biosynthesis of C7 Backbone

[0182] In some embodiments, glutaryl-CoA is synthesized from the central metabolite, acetyl-CoA, by conversion of acetyl-CoA to acetoacetyl-CoA by a .beta.-ketothiolase classified, for example, under EC 2.3.1.9 such as the gene product of atoB or phaA or by an acetyl-CoA carboxylase classified under, for example, EC 6.4.1.2 and an acetoacetyl-CoA synthase classified, for example, under EC 2.3.1.194; followed by conversion to 3-hydroxybutanoyl-CoA by a 3-hydroxyacyl-CoA dehydrogenase classified, for example, under EC 1.1.1.- such as EC 1.1.1.157 or EC 1.1.1.35 such as the gene product of hbd; followed by conversion to crotonyl-CoA by an enoyl-CoA reductase classified, for example, under EC 4.2.1.- (e.g., EC 4.2.1.17) such as the gene product of crt, followed by conversion to either a) glutaconyl-CoA by a glutaconyl-CoA decarboxylase classified, for example, under EC 4.1.1.70; followed by conversion to glutaryl-CoA by either (i) an enoyl-[acp]reductase classified, for example, under EC 1.3.1.9 or (ii) a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44 such as the gene product of ter or tdter or (b) glutaryl-CoA by a glutaryl-CoA dehydrogenase subject to electron bifurcation from Synthrophus aciditrophicus such as the dehydrogenases of Genbank Accession Nos. (1) ABC77899.1, (2) ABC76101.1, (3) ABC76260.1, (4) ABC76949.1 or (5) ABC78863.1. See, FIG. 1.

[0183] In some embodiments, glutaryl-CoA can be synthesized from the central metabolite, 2-oxo-glutarate, by conversion of 2-oxo-glutrate to (Homo).sub.1citrate by a homocitrate synthase classified, for example, under EC 2.3.3.14 or EC 2.3.3.13 such as the gene product of LYS20 and LYS21 from Saccharomyces cerevisiae or hcs from Thermus thermophiles; followed by conversion to iso(homo).sub.1citrate by a homocitrate dehydratase and a homoaconitate hydratase classified, for example, under EC 4.2.1.114, EC 4.2.1.36 or EC 4.2.1.33 such as the gene product of LYS4 from Saccharomyces cerevisiae or lysT and LysU from Thermus thermophiles; followed by conversion to 2-oxoadipate by an iso(homo).sub.ncitrate dehydrogenase classified, for example, under EC 1.1.1.85, EC 1.1.1.87 or EC 1.1.1.286 such as the gene product of LYS12 from Saccharomyces cerevisiae or hicdh from Thermus thermophiles; followed by conversion to glutarate semialdehyde by a decarboxylase classified, for example under EC 4.1.1.43, EC 4.1.1.74, EC 4.1.1.72 such as an indolepyruvate decarboxylase (e.g., GenBank Accession No. CAC48239.1), a branched-chain alpha-ketoacid decarboxylase (e.g., Genbank Accession No. AAS49166.1) or an alpha-ketoisovalerate decarboxylase (e.g., Genbank Accession No. ADA65057.1); followed by conversion to glutarate by a glutarate semialdehyde dehydrogenase classified, for example, under EC 1.2.1.20, EC 1.2.1.16, EC 1.2.1.79, EC 1.2.1.3, or EC 1.2.1.63 such as the gene product of CpnE, ChnE, or ThnG; followed by conversion to glutaryl-CoA by a glutarate:CoA ligase classified, for example, under EC 6.2.1.6 or by a CoA-transferase classified, for example, under EC 2.8.3.12. See, e.g., FIG. 1.

[0184] In some embodiments, pimeloyl-CoA can be synthesized from glutaryl-CoA produced as described above by conversion of glutaryl-CoA to 3-ketopimeloyl-CoA by a .beta.-ketothiolase classified under EC 2.3.1.-, e.g., EC 2.3.1.174 or EC 2.3.1.16 such as the gene product of paaJ or homologs of paaJ (e.g., Genbank Accession No. ABC78517.1, AAC74479.1, or ABC78881.1) or by a .beta.-ketoacyl-[acp]synthase classified, for example, under EC 2.3.1.41, EC 2.3.1.179, EC 2.3.1.180; followed by conversion to 3-hydroxypimeloyl-CoA by a 3-hydroxyadipyl-CoA dehydrogenase classified, for example, under EC 1.1.1.157 such as the gene product of paaH or homologs of paaH (e.g., Genbank Accession No. ABC77793.1); followed by conversion to 2(E)-heptenedioyl-CoA (also known as 2,3-dehydropimeloyl-CoA) by an enoyl-CoA hydratase such as the gene product of paaF or homologs of paaF (e.g., Genbank Accession No. ABC77794.1 or Genbank Accession No. ABC78950.1); followed by conversion to 2(E)-heptenedioate by an acyl-[acp]thioesterase classified under EC 3.1.2.-, such as the acyl-[acp]thioesterase from Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO: 4) or from Lactobacillus plantarum (GenBank Accession No. CCC78182.1, SEQ ID NO: 5) or CoA-transferase classified under EC 2.8.3.- such as EC 2.8.3.12 (see, e.g., Genbank Accession No. CAA57199.1 (GctA) and CAA57200.1 (GctB), SEQ ID NOs: 24 and 25, respectively), followed by conversion to 2(E)-heptenedioate methyl ester using a fatty acid O-methyltransferase classified, for example, under EC 2.1.1.15 such as the fatty acid O-methyltransferase from Mycobacterium marinum M (GenBank Accession No. ACC41782.1, SEQ ID NO: 1); Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 2), or Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 3); followed by conversion to 2(E)-heptenedioyl-CoA methyl ester by a CoA ligase classified, for example, under EC 6.2.1.- (e.g., a butyrate-CoA ligase classified under EC 6.2.1.2 or a long-chain-fatty-acid-CoA ligase classified under EC 6.2.1.3); followed by conversion to pimeloyl-CoA methyl ester using a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44 such as the gene product of ter or tdter; followed by conversion to pimeloyl-CoA by a pimelyl-[acp]methyl ester esterase classified, for example, under EC 3.1.1.85 such as the gene product of bioH from E. coli. (GenBank Accession No. AAC76437.1, SEQ ID NO: 6). See, e.g., FIG. 1.

[0185] In some embodiments, pimeloyl-CoA can be synthesized from the central metabolite, 2-oxo-glutarate, by two cycles of 2-oxoacid chain elongation by conversion of 2-oxoglutrate to (Homo).sub.1citrate by a (Homo).sub.ncitrate synthase classified, for example, under EC 2.3.3.14 or EC 2.3.3.13 (see, e.g., AksA, Genbank Accession No. AAB98494.1); followed by conversion to iso(homo).sub.1citrate by a (homo).sub.ncitrate dehydratase and a (homo).sub.naconitate hydratase classified, for example, under EC 4.2.1.114, EC 4.2.1.36 or EC 4.2.1.33 (see, e.g., AksD and AksE, Genbank Accession Nos. AAB99007.1 and AAB99277.1); followed by conversion to 2-oxoadipate by an iso(homo).sub.ncitrate dehydrogenase classified, for example, under EC 1.1.1.85, EC 1.1.1.87 or EC 1.1.1.286 (see, e.g., AksF, Genbank Accession No. ACA28837.1); followed by conversion to (Homo).sub.2citrate by a (Homo).sub.ncitrate synthase classified, for example, under EC 2.3.3.14 or EC 2.3.3.13 (see, e.g., AksA, Genbank Accession No. AAB98494.1); followed by conversion to iso(homo).sub.2citrate (also known as 1-hydroxypentane-1,2,5-tricarboxylate or threo-iso(homo).sub.2citrate) by a (homo).sub.ncitrate dehydratase and a (homo).sub.naconitate hydratase classified, for example, under EC 4.2.1.114, EC 4.2.1.36 or EC 4.2.1.33 (see, e.g., Genbank Accession Nos. AAB99007.1 and AAB99277.1); followed by conversion to 2-oxo-pimelate by an iso(homo).sub.ncitrate dehydrogenase classified under, for example, EC 1.1.1.85, EC 1.1.1.87, or EC 1.1.1.286 (see, e.g., AksF, Genbank Accession No. ACA28837.1); followed by conversion to 2-oxo-pimelate using an alcohol dehydrogenase classified under EC 1.1.1.- such as the gene product of HgdH (see Djurdjevic et al, 2011, supra) or LdhA (see Kim et al., 2005, FEBS Journal, 272, 550-561); followed by conversion to 2-hydroxypimeloyl-CoA by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 (e.g., the gene product of GctAB); followed by conversion to 2(E)-heptenedioyl-CoA by a 2-hydroxyglutaryl-CoA dehydratase classified, for example, under EC 4.2.1.- such as the gene product of HgdAB in combination with its activator, the gene product of HgdC (see Djurdjevic et al, 2011, supra) or a 2-hydroxyisocaproyl-CoA dehydratase classified, for example, under EC 4.2.1.- such as the gene product of hadBC in combination with its activator, the gene product of hadI (Kim et al., 2005, supra); followed by conversion to 2(E)-heptenedioate by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 (e.g., the gene product of GctAB); followed by conversion to 2(E)-heptenedioate methyl ester using a fatty acid O-methyltransferase classified, for example, under EC 2.1.1.15 such as the fatty acid O-methyltransferase from Mycobacterium marinum M (GenBank Accession No. ACC41782.1, SEQ ID NO: 1); Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 2), or Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 3); followed by conversion to 2(E)-heptenedioyl-CoA methyl ester by a CoA ligase classified, for example, under EC 6.2.1.- (e.g., a butyrate-CoA ligase classified under EC 6.2.1.2 or a long-chain-fatty-acid-CoA ligase classified under EC 6.2.1.3); followed by conversion to pimeloyl-CoA methyl ester using a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44 such as the gene product of ter or tdter; followed by conversion to pimeloyl-CoA by a pimelyl-[acp]methyl ester esterase classified, for example, under EC 3.1.1.85 such as the gene product of bioH from E. coli. (GenBank Accession No. AAC76437.1, SEQ ID NO: 6). See, e.g., FIG. 2.

Pathway Using Succinate Semialdehyde as Central Metabolite in the Biosynthesis of C7 Backbone

[0186] In some embodiments, pimeloyl-CoA can be synthesized from (i) the central metabolite 2-oxoglutarate by conversion of 2-oxoglutarate to succinate semialdehyde by a branched-chain alpha-ketoacid decarboxylase (e.g., Genbank Accession No. AAS49166.1) classified, for example, under EC 4.1.1.72 or an alpha-ketoisovalerate decarboxylase (e.g., Genbank Accession No. ADA65057.1) classified, for example, under EC 4.1.1.74 or from (ii) the central metabolite succinyl-CoA by conversion of succinyl-CoA to succinate semialdehyde by a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.76; followed by conversion to 2,4-dihydroxyhept-2-enedioate by a 4-hydroxy-2-oxoheptanedioate aldolase classified, for example, under EC 4.1.2.52 (e.g., the gene product of HpaI); followed by conversion to 2-oxohept-3-enedioate by a 2-oxo-hept-3-ene-1,7-dioate hydratase classified, for example, under EC 4.2.1.- such as the gene product of HpaH (e.g., Genbank Accession No. AAB91474.1); followed by conversion to 2-oxopimelate by a 2-enoate reductase classified under EC 1.3.1.- such as EC 1.3.1.31 or EC 1.6.99.- such as EC 1.6.99.1 (e.g., encoded by Genbank Accession Nos. BAA12619.1, AAN66878.1, AAA98815.1, AGP69310.1, CAA37666.1, ABY93685.1, or AAB38683.1); followed by conversion to 2-hydroxypimelate by a 2-hydroxyglutarate dehydrogenase classified, for example under EC 1.1.1.- such as EC 1.1.1.337 (e.g., the gene product of HgdH or ldhA); followed by conversion to 2-hydroxypimeloyl-CoA by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 (e.g., the gene product of GctAB); followed by conversion to 2(E)-heptenedioyl-CoA by a 2-hydroxyglutaryl-CoA dehydratase classified, for example, under EC 4.2.1.- such as the gene product of HgdAB in combination with its activator, the gene product of HgdC (see, Djurdjevic et al, 2011, supra) or a 2-hydroxyisocaproyl-CoA dehydratase classified, for example, under EC 4.2.1.- such as the gene product of hadBC in combination with its activator, the gene product of hadI (Kim et al., 2005, supra); followed by conversion to 2(E)-heptenedioate by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 (e.g., the gene product of GctAB); followed by conversion to 2(E)-heptenedioate methyl ester using a fatty acid O-methyltransferase classified, for example, under EC 2.1.1.15 such as the fatty acid O-methyltransferase from Mycobacterium marinum (GenBank Accession No. ACC41782.1. SEQ ID NO: 1); Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 2), or Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 3); followed by conversion to 2(E)-heptenedioyl-CoA methyl ester by a CoA ligase classified, for example, under EC 6.2.1.- such as a butyrate-CoA ligase classified, for example, under EC 6.2.1.2 or a long-chain-fatty-acid-CoA ligase classified, for example, under EC 6.2.1.3 (e.g. Genbank Accession No. CAA50321.1 or CAJ95550.1); followed by conversion to pimeloyl-CoA methyl ester using a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44 such as the gene product of ter (e.g., Genbank Accession No. AAW66853.1) or tdter (Genbank Accession No. AAS11092.1); followed by conversion to pimeloyl-CoA by a pimelyl-[acp]methyl ester esterase classified, for example, under EC 3.1.1.85 such as the gene product of bioH from E. coli. (GenBank Accession No. AAC76437.1, SEQ ID NO: 6). See, e.g., FIG. 3.

Pathways Using Pimeloyl-CoA or Pimelate Semialdehyde as Central Precursors to Pimelate

[0187] In some embodiments, pimelic acid is synthesized from the central precursor pimeloyl-CoA by conversion of pimeloyl-CoA to pimelate semialdehyde by an acetylating aldehyde dehydrogenase classified, for example, under EC 1.2.1.10 such as the gene product of PduB or PduP (see, for example, Lan et al., 2013, Energy Environ. Sci., 6:2672-2681); followed by conversion to pimelic acid by a 7-oxoheptanoate dehydrogenase classified, for example, under EC 1.2.1.- such as the gene product of ThnG, a 6-oxohexanoate dehydrogenase classified, for example, under EC 1.2.1.63 such as the gene product of ChnE, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.- such as the gene product of CpnE, or an aldehyde dehydrogenase (classified, for example, under EC 1.2.1.3). See, FIG. 4.

[0188] In some embodiments, pimelic acid is synthesized from the central precursor pimeloyl-CoA by conversion of pimeloyl-CoA to pimelate by a thioesterase classified, for example, under EC 3.1.2.- such as the gene products of YciA, tesB (Genbank Accession No. AAA24665.1, SEQ ID NO: 21), Acot13, an acyl-[acp]thioesterase from Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO: 4), or an acyl-[acp]thioesterase from Lactobacillus plantarum (GenBank Accession No. CCC78182.1, SEQ ID NO: 5). See, FIG. 4.

[0189] In some embodiments, pimelate is synthesized from the central precursor pimeloyl-CoA by conversion of pimeloyl-CoA to pimelate by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12. See, FIG. 4.

[0190] In some embodiments, pimelate is synthesized from the central precursor pimeloyl-CoA by conversion of pimeloyl-CoA to pimelate by a reversible CoA-ligase such as a reversible succinate CoA-ligase classified, for example, under EC 6.2.1.5. See, FIG. 4.

Pathways Using Pimeloyl-CoA or Pimelate Semialdehyde as Central Precursor to 7-Aminoheptanoate

[0191] In some embodiments, 7-aminoheptanoate is synthesized from the central precursor pimeloyl-CoA by conversion of pimeloyl-CoA to pimelate semialdehyde by an acetylating aldehyde dehydrogenase classified, for example, EC 1.2.1.10, such as the gene product of PduB or PduP; followed by conversion of pimelate semialdehyde to 7-aminoheptanoate by a .omega.-transaminase classified, for example, under EC 2.6.1.- such as EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18). See, FIG. 5.

[0192] In some embodiments, 7-aminoheptanoate is synthesized from the central precursor pimelate by conversion of pimelate to pimelate semialdehyde by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from Segniliparus rugosus (Genbank Accession No. EFV11917.1, SEQ ID NO: 9) or Segniliparus rotundus (Genbank Accession No. ADG98140.1, SEQ ID NO: 12), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia), or the gene products of GriC and GriD from Streptomyces griseus (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of pimelate semialdehyde to 7-aminoheptanoate by a co-transaminase classified, for example, under EC 2.6.1.- such as EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.48, EC 2.6.1.29, EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18). See, FIG. 5.

Pathway Using 7-Aminoheptanoate, 7-Hydroxyheptanoate or Pimelate Semialdehyde as Central Precursor to Heptamethylenediamine

[0193] In some embodiments, heptamethylenediamine is synthesized from the central precursor 7-aminoheptanoate by conversion of 7-aminoheptanoate to 7-aminoheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car (see above) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia) or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 7-aminoheptanal to heptamethylenediamine by a .omega.-transaminase classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 14), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 17), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18). See FIG. 6.

[0194] The carboxylate reductase encoded by the gene product of car and the phosphopantetheine transferase enhancer npt or sfp has broad substrate specificity, including terminal difunctional C4 and C5 carboxylic acids (Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42, 130-137).

[0195] In some embodiments, heptamethylenediamine is synthesized from the central precursor 7-hydroxyheptanoate (which can be produced as described in FIG. 7), by conversion of 7-hydroxyheptanoate to 7-hydroxyheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 7), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 8), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1, SEQ ID NO: 9), a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 10), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 11), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 12), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 7-aminoheptanal to 7-aminoheptanol by a .omega.-transaminase classified, for example, under EC 2.6.1.- such as EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), or a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16); followed by conversion to 7-aminoheptanal by an alcohol dehydrogenase classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (classified, for example, under EC 1.1.1.2, see Genbank Accession No. CAA90836.1) (classified, for example, under EC 1.1.1.2, see Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1 (from Geobacillus stearothermophilus); followed by conversion to heptamethylenediamine by a .omega.-transaminase classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 14), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 17), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18). See FIG. 6.

[0196] In some embodiments, heptamethylenediamine is synthesized from the central precursor 7-aminoheptanoate by conversion of 7-aminoheptanoate to N7-acetyl-7-aminoheptanoate by a N-acetyltransferase such as a lysine N-acetyltransferase classified, for example, under EC 2.3.1.32; followed by conversion to N7-acetyl-7-aminoheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 8), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 11), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 12), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion to N7-acetyl-1,7-diaminoheptane by a .omega.-transaminase classified, for example, under EC 2.6.1.- such as EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, EC 2.6.1.46, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 14), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 17), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18); followed by conversion to heptamethylenediamine by an acetylputrescine deacetylase classified, for example, under EC 3.5.1.62 or EC 3.5.1.17. See, FIG. 6.

[0197] In some embodiments, heptamethylenediamine is synthesized from the central precursor pimelate semialdehyde by conversion of pimelate semialdehyde to heptanedial by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 12), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion to 7-aminoheptanal by a .omega.-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82; followed by conversion to heptamethylenediamine by a .omega.-transaminase classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 13), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 14), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 15), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 16), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 17), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 18). See FIG. 6.

Pathways Using Pimelate or Pimelate Semialdehyde as Central Precursor to 7-Hydroxyheptanoic Acid and 1,7-Heptanediol

[0198] In some embodiments, 7-hydroxyheptanoate is synthesized from the central precursor pimelate by conversion of pimelate to pimelate semialdehyde by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from Segniliparus rugosus (Genbank Accession No. EFV11917.1, SEQ ID NO: 9) or Segniliparus rotundus (Genbank Accession No. ADG98140.1, SEQ ID NO: 12), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia), or the gene products of GriC and GriD from Streptomyces griseus; followed by conversion to 7-hydroxyheptanoate by an alcohol dehydrogenase classified, for example, under EC 1.1.1.- such as a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258 (e.g., the gene from of ChnD), a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.- such as the gene product of CpnD (see, for example, Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684), a 5-hydroxypentanoate dehydrogenase from Clostridium viride, or a 4-hydroxybutyrate dehydrogenase such as gabD (see, for example, Lutke-Eversloh & Steinbuchel, 1999, FEMS Microbiology Letters, 181(1):63-71). See, FIG. 7.

[0199] In some embodiments, 7-hydroxyheptanoate is synthesized from the central precursor pimeloyl-CoA by conversion of pimeloyl-CoA to pimelate semialdehyde by an acetylating aldehyde dehydrogenase classified, for example, under EC 1.2.1.10 such as the gene product of PduB or PduP; followed by conversion to 7-hydroxyheptanoate by an alcohol dehydrogenase classified, for example, under EC 1.1.1.- such as a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258 (e.g., the gene from of ChnD), a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.- such as the gene product of CpnD, a 5-hydroxypentanoate dehydrogenase from Clostridium viride, or a 4-hydroxybutyrate dehydrogenase such as gabD. See, also FIG. 7.

[0200] In some embodiments, 1,7 heptanediol is synthesized from the central precursor 7-hydroxyheptanoate by conversion of 7-hydroxyheptanoate to 7-hydroxyheptanal by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 7), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 8), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1, SEQ ID NO: 9), a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 10), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 11), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 12), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO: 19) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO: 20) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 7-hydroxyheptanal to 1,7 heptanediol by an alcohol dehydrogenase classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (classified, for example, under EC 1.1.1.2, see Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1 (from Geobacillus stearothermophilus). See, FIG. 8.

Cultivation Strategy

[0201] In some embodiments, the cultivation strategy entails achieving an aerobic, anaerobic, micro-aerobic, or mixed oxygen/denitrification cultivation condition. Enzymes characterized in vitro as being oxygen sensitive require a micro-aerobic cultivation strategy maintaining a very low dissolved oxygen concentration (See, for example, Chayabatra & Lu-Kwang, Appl. Environ. Microbiol., 2000, 66(2), 493-498; Wilson and Bouwer, 1997, Journal of Industrial Microbiology and Biotechnology, 18(2-3), 116-130).

[0202] In some embodiments, the cultivation strategy entails nutrient limitation such as nitrogen, phosphate or oxygen limitation.

[0203] In some embodiments, a final electron acceptor other than oxygen such as nitrates can be utilized.

[0204] In some embodiments, a cell retention strategy using, for example, ceramic membranes can be employed to achieve and maintain a high cell density during either fed-batch or continuous fermentation.

[0205] In some embodiments, the principal carbon source fed to the fermentation in the synthesis of one or more C7 building blocks can derive from biological or non-biological feedstocks.

[0206] In some embodiments, the biological feedstock can be, can include, or can derive from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.

[0207] The efficient catabolism of crude glycerol stemming from the production of biodiesel has been demonstrated in several microorganisms such as Escherichia coli, Cupriavidus necator, Pseudomonas oleavorans, Pseudomonas putida and Yarrowia lipolytica (Lee et al., Appl. Biochem. Biotechnol., 2012, 166, 1801-1813; Yang et al., Biotechnology for Biofuels, 2012, 5:13; Meijnen et al., Appl. Microbiol. Biotechnol., 2011, 90, 885-893).

[0208] The efficient catabolism of lignocellulosic-derived levulinic acid has been demonstrated in several organisms such as Cupriavidus necator and Pseudomonas putida in the synthesis of 3-hydroxyvalerate via the precursor propanoyl-CoA (Jaremko and Yu, Journal of Biotechnology, 2011, 155, 2011, 293-298; Martin and Prather, Journal of Biotechnology, 2009, 139, 61-67).

[0209] The efficient catabolism of lignin-derived aromatic compounds such as benzoate analogues has been demonstrated in several microorganisms such as Pseudomonas putida, Cupriavidus necator (Bugg et al., Current Opinion in Biotechnology, 2011, 22, 394-400; Perez-Pantoja et al., FEMS Microbiol. Rev., 2008, 32, 736-794).

[0210] The efficient utilization of agricultural waste, such as olive mill waste water has been demonstrated in several microorganisms, including Yarrowia lipolytica (Papanikolaou et al., Bioresour. Technol., 2008, 99(7), 2419-2428).

[0211] The efficient utilization of fermentable sugars such as monosaccharides and disaccharides derived from cellulosic, hemicellulosic, cane and beet molasses, cassava, corn and other agricultural sources has been demonstrated for several microorganism such as Escherichia coli, Corynebacterium glutamicum and Lactobacillus delbrueckii and Lactococcus lactis (see, e.g., Hermann et al, Journal of Biotechnology, 2003, 104, 155-172; Wee et al., Food Technol. Biotechnol., 2006, 44(2), 163-172; Ohashi et al., Journal of Bioscience and Bioengineering, 1999, 87(5), 647-654).

[0212] The efficient utilization of furfural, derived from a variety of agricultural lignocellulosic sources, has been demonstrated for Cupriavidus necator (Li et al., Biodegradation, 2011, 22, 1215-1225).

[0213] In some embodiments, the non-biological feedstock can be or can derive from natural gas, syngas, CO.sub.2/H.sub.2, methanol, ethanol, benzoic acid, non-volatile residue (NVR), a caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

[0214] The efficient catabolism of methanol has been demonstrated for the methylotrophic yeast Pichia pastoris.

[0215] The efficient catabolism of ethanol has been demonstrated for Clostridium kluyveri (Seedorf et al., Proc. Natl. Acad. Sci. USA, 2008, 105(6) 2128-2133).

[0216] The efficient catabolism of CO.sub.2 and H.sub.2, which may be derived from natural gas and other chemical and petrochemical sources, has been demonstrated for Cupriavidus necator (Prybylski et al., Energy, Sustainability and Society, 2012, 2:11).

[0217] The efficient catabolism of syngas has been demonstrated for numerous microorganisms, such as Clostridium ljungdahlii and Clostridium autoethanogenum (Kopke et al., Applied and Environmental Microbiology, 2011, 77(15), 5467-5475).

[0218] The efficient catabolism of the non-volatile residue waste stream from cyclohexane processes has been demonstrated for numerous microorganisms, such as Delftia acidovorans and Cupriavidus necator (Ramsay et al., Applied and Environmental Microbiology, 1986, 52(1), 152-156). In some embodiments, the host microorganism is a prokaryote. For example, the prokaryote can be a bacterium from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia such as Delftia acidovorans; from the genus Bacillus such as Bacillus subtillis; from the genus Lactobacillus such as Lactobacillus delbrueckii; or from the genus Lactococcus such as Lactococcus lactis. Such prokaryotes also can be a source of genes to construct recombinant host cells described herein that are capable of producing one or more C7 building blocks.

[0219] In some embodiments, the host microorganism is a eukaryote. For example, the eukaryote can be a filamentous fungus, e.g., one from the genus Aspergillus such as Aspergillus niger. Alternatively, the eukaryote can be a yeast, e.g., one from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; or from the genus Yarrowia such as Yarrowia lipolytica; from the genus Issatchenkia such as Issathenkia orientalis; from the genus Debaryomyces such as Debaryomyces hansenii; from the genus Arxula such as Arxula adenoinivorans; or from the genus Kluyveromyces such as Kluyveromyces lactis. Such eukaryotes also can be a source of genes to construct recombinant host cells described herein that are capable of producing one or more C7 building blocks.

Metabolic Engineering

[0220] The present document provides methods involving less than all the steps described for all the above pathways. Such methods can involve, for example, one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more of such steps. Where less than all the steps are included in such a method, the first, and in some embodiments the only, step can be any one of the steps listed.

[0221] Furthermore, recombinant hosts described herein can include any combination of the above enzymes such that one or more of the steps, e.g., one, two, three, four, five, six, seven, eight, nine, ten, or more of such steps, can be performed within a recombinant host. This document provides host cells of any of the genera and species listed and genetically engineered to express one or more (e.g., two, three, four, five, six, seven, eight, nine, 10, 11, 12 or more) recombinant forms of any of the enzymes recited in the document. Thus, for example, the host cells can contain exogenous nucleic acids encoding enzymes catalyzing one or more of the steps of any of the pathways described herein.

[0222] In addition, this document recognizes that where enzymes have been described as accepting CoA-activated substrates, analogous enzyme activities associated with [acp]-bound substrates exist that are not necessarily in the same enzyme class.

[0223] Also, this document recognizes that where enzymes have been described accepting (R)-enantiomers of substrate, analogous enzyme activities associated with (S)-enantiomer substrates exist that are not necessarily in the same enzyme class.

[0224] This document also recognizes that where an enzyme is shown to accept a particular co-factor, such as NADPH, or a co-substrate, such as acetyl-CoA, many enzymes are promiscuous in terms of accepting a number of different co-factors or co-substrates in catalyzing a particular enzyme activity. Also, this document recognizes that where enzymes have high specificity for e.g., a particular co-factor such as NADH, an enzyme with similar or identical activity that has high specificity for the co-factor NADPH may be in a different enzyme class.

[0225] In some embodiments, the enzymes in the pathways outlined herein are the result of enzyme engineering via non-direct or rational enzyme design approaches with aims of improving activity, improving specificity, reducing feedback inhibition, reducing repression, improving enzyme solubility, changing stereo-specificity, or changing co-factor specificity.

[0226] In some embodiments, the enzymes in the pathways outlined herein can be gene dosed (i.e., overexpressed by having a plurality of copies of the gene in the host organism), into the resulting genetically modified organism via episomal or chromosomal integration approaches.

[0227] In some embodiments, genome-scale system biology techniques such as Flux Balance Analysis can be utilized to devise genome scale attenuation or knockout strategies for directing carbon flux to a C7 building block.

[0228] Attenuation strategies include, but are not limited to; the use of transposons, homologous recombination (double cross-over approach), mutagenesis, enzyme inhibitors and RNA interference (RNAi).

[0229] In some embodiments, fluxomic, metabolomic and transcriptomal data can be utilized to inform or support genome-scale system biology techniques, thereby devising genome scale attenuation or knockout strategies in directing carbon flux to a C7 building block.

[0230] In some embodiments, the host microorganism's tolerance to high concentrations of a C7 building block can be improved through continuous cultivation in a selective environment.

[0231] In some embodiments (see, e.g., FIGS. 1 to 3), the host microorganism's endogenous biochemical network can be attenuated or augmented (1) to ensure the intracellular availability of 2-oxo-glutarate and acetyl-CoA; (2) to create an NADPH imbalance that may be balanced via the formation of a C7 building block; (3) to prevent degradation of central metabolites or central precursors leading to and including C7 building blocks; and/or (4) to ensure efficient efflux from the cell.

[0232] In some embodiments requiring the intracellular availability of 2-oxo-glutarate, a PEP carboxykinase or PEP carboxylase can be overexpressed in the host to generate anaplerotic carbon flux into the Krebs cycle towards 2-oxo-glutarate (Schwartz et al., 2009, Proteomics, 9, 5132-5142).

[0233] In some embodiments requiring the intracellular availability of 2-oxo-glutarate, a pyruvate carboxylase can be overexpressed in the host to generated anaplerotic carbon flux into the Krebs cycle towards 2-oxoglutarate (Schwartz et al., 2009, Proteomics, 9, 5132-5142).

[0234] In some embodiments requiring the intracellular availability of 2-oxo-glutarate, a PEP synthase can be overexpressed in the host to enhance the flux from pyruvate to PEP, thus increasing the carbon flux into the Krebs cycle via PEP carboxykinase or PEP carboxylase (Schwartz et al., 2009, Proteomics, 9, 5132-5142).

[0235] In some embodiments requiring the intracellular availability of 2-oxoglutarate for C6 building block synthesis, anaplerotic reactions enzymes such as phosphoenolpyruvate carboxylase (e.g., the gene product of pck), phosphoenolpyruvate carboxykinase (e.g., the gene product of ppc), the malic enzyme (e.g., the gene product of sfcA) and/or pyruvate carboxylase are overexpressed in the host organisms (Song and Lee, 2006, Enzyme Micr. Technol., 39, 352-361).

[0236] In some embodiments requiring intracellular availability of acetyl-CoA, endogenous enzymes catalyzing the hydrolysis of acetyl-CoA such as short-chain length thioesterases (e.g., an acetyl-CoA thioesterase) can be attenuated in the host organism.

[0237] In some embodiments requiring condensation of acetyl-CoA for C7 building block synthesis, one or more endogenous .beta.-ketothiolases catalyzing the condensation of only acetyl-CoA to acetoacetyl-CoA such as the endogenous gene products of AtoB or phaA can be attenuated.

[0238] In some embodiments requiring the intracellular availability of acetyl-CoA, an endogenous phosphotransacetylase generating acetate such as pta can be attenuated (Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).

[0239] In some embodiments requiring the intracellular availability of acetyl-CoA, an endogenous gene in an acetate synthesis pathway encoding an acetate kinase, such as ack, can be attenuated.

[0240] In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to lactate such as a lactate dehydrogenase encoded by ldhA can be attenuated (Shen et al., 2011, supra).

[0241] In some embodiments requiring the intracellular availability of Krebs cycle intermediates for C6 building block synthesis, 2-oxoglutarate dehydrogenase is attenuated in one or more of its subunits.

[0242] In some embodiments requiring intracellular availability of Krebs cycle intermediates for C6 building block synthesis, the regulator of 2-oxoglutarate dehydrogenase is overexpressed by induction in the host microorganism.

[0243] In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, endogenous genes encoding enzymes, such as menaquinol-fumarate oxidoreductase, that catalyze the degradation of phophoenolpyruvate to succinate such as frdBC can be attenuated (see, e.g., Shen et al., 2011, supra).

[0244] In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of acetyl-CoA to ethanol such as the alcohol dehydrogenase encoded by adhE can be attenuated (Shen et al., 2011, supra).

[0245] In some embodiments where the host microorganism uses the lysine biosynthesis pathway via meso-2,6-diaminopimelate, the genes encoding the synthesis of 2-oxoadipate from 2-oxoglutarate are gene dosed into the host.

[0246] In some embodiments where the host microorganism uses the lysine biosynthesis pathway via 2-oxoadipate, the genes encoding the synthesis of lysine via meso-2,6-diaminopimelate are gene dosed into the host.

[0247] In some embodiments, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to ethanol such as pyruvate decarboxylase is attenuated.

[0248] In some embodiments, where pathways require excess NADPH or NADH co-factor for C7 building block synthesis, an endogenous transhydrogenase such as one classified under EC 1.6.1.1, EC 1.6.1.2, or EC 1.6.1.3, dissipating the co-factor imbalance can be attenuated.

[0249] In some embodiments, where pathways require excess NADPH co-factor for C7 building block synthesis, an exogenous transhydrogenase such as one classified under EC 1.6.1.1, EC 1.6.1.2 or EC 1.6.1.3, converting NADH to NADPH can be overexpressed.

[0250] In some embodiments using hosts that naturally accumulate polyhydroxyalkanoates, an endogenous gene encoding a polyhydroxyalkanoate synthase enzyme can be attenuated in the host strain.

[0251] In some embodiments using hosts that naturally accumulate lipid bodies, the genes encoding enzymes involved with lipid body synthesis are attenuated.

[0252] In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, a recombinant acetyl-CoA synthetase such as the gene product of acs can be overexpressed in the microorganism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).

[0253] In some embodiments, an L-alanine dehydrogenase can be overexpressed in the host to regenerate L-alanine from pyruvate as amino donor for .omega.-transaminase reactions.

[0254] In some embodiments, a NADH-specific L-glutamate dehydrogenase can be overexpressed in the host to regenerate L-glutamate from 2-oxo-glutarate as amino donor for .omega.-transaminase reactions.

[0255] In some embodiments, enzymes such as pimeloyl-CoA dehydrogenase classified under, for example, EC 1.3.1.62; an acyl-CoA dehydrogenase classified under, for example, EC 1.3.8.7 or EC 1.3.8.1; and/or a glutaryl-CoA dehydrogenase classified under, for example, EC 1.3.8.6 that degrade central metabolites and central precursors leading to and including C7 building blocks can be attenuated.

[0256] In some embodiments, endogenous enzymes activating C7 building blocks via Coenzyme A esterification such as CoA-ligases such as pimeloyl-CoA synthetase classified under, for example, EC 6.2.1.14 can be attenuated.

[0257] In some embodiments, carbon flux can be directed into the pentose phosphate cycle to increase the supply of NADPH by attenuating an endogenous glucose-6-phosphate isomerase (EC 5.3.1.9).

[0258] In some embodiments, carbon flux can be redirected into the pentose phosphate cycle to increase the supply of NADPH by overexpression a 6-phosphogluconate dehydrogenase and/or a transketolase (Lee et al., 2003, Biotechnology Progress, 19(5), 1444-1449).

[0259] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a gene such as UdhA encoding a puridine nucleotide transhydrogenase can be overexpressed in the host organisms (Brigham et al., Advanced Biofuels and Bioproducts, 2012, Chapter 39, 1065-1090).

[0260] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 Building Block, a recombinant glyceraldehyde-3-phosphate-dehydrogenase gene such as GapN can be overexpressed in the host organisms (Brigham et al., 2012, supra).

[0261] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant malic enzyme gene such as maeA or maeB can be overexpressed in the host organisms (Brigham et al., 2012, supra).

[0262] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant glucose-6-phosphate dehydrogenase gene such as zwf can be overexpressed in the host organisms (Lim et al., J. Bioscience and Bioengineering, 2002, 93(6), 543-549).

[0263] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant fructose 1,6 diphosphatase gene such as fbp can be overexpressed in the host organisms (Becker et al., J. Biotechnol., 2007, 132:99-109).

[0264] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, endogenous triose phosphate isomerase (EC 5.3.1.1) can be attenuated.

[0265] In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant glucose dehydrogenase such as the gene product of gdh can be overexpressed in the host organism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).

[0266] In some embodiments, endogenous enzymes facilitating the conversion of NADPH to NADH can be attenuated, such as the NADH generation cycle that may be generated via inter-conversion of glutamate dehydrogenases classified under EC 1.4.1.2 (NADH-specific) and EC 1.4.1.4 (NADPH-specific). For example, avoiding dissipation of an NADPH imbalance towards C7 building blocks, a NADH-specific glutamate dehydrogenase can be attenuated.

[0267] In some embodiments, an endogenous glutamate dehydrogenase (EC 1.4.1.3) that utilizes both NADH and NADPH as co-factors can be attenuated.

[0268] In some embodiments, a methanol dehydrogenase or a formaldehyde dehydrogenase can be overexpressed in the host to allow methanol catabolism via formate.

[0269] In some embodiments, a S-adenosylmethionine synthetase can be overexpressed in the host to generate S-Adenosyl-L-methionine as a co-factor for a fatty acid O-methyltransferase.

[0270] In some embodiments, one or more of 3-phosphoglycerate dehydrogenase, 3-phosphoserine aminotransferase and phosphoserine phosphatase can be overexpressed in the host to generate serine as a methyl donor for the S-Adenosyl-L-methionine cycle.

[0271] In some embodiments, a membrane-bound enoyl-CoA reductases can be solubilized via expression as a fusion protein to a small soluble protein such as a maltose binding protein (Gloerich et al., FEBS Letters, 2006, 580, 2092-2096).

[0272] In some embodiments, the efflux of a C7 building block across the cell membrane to the extracellular media can be enhanced or amplified by genetically engineering structural modifications to the cell membrane or increasing any associated transporter activity for a C7 building block.

[0273] The efflux of heptamethylenediamine can be enhanced or amplified by overexpressing broad substrate range multidrug transporters such as Blt from Bacillus subtilis (Woolridge et al., 1997, J. Biol. Chem., 272(14):8864-8866); AcrB and AcrD from Escherichia coli (Elkins & Nikaido, 2002, J. Bacteriol., 184(23), 6490-6499) or NorA from Staphylococcus aereus (Ng et al., 1994, Antimicrob Agents Chemother, 38(6), 1345-1355) or Bmr from Bacillus subtilis (Neyfakh, 1992, Antimicrob Agents Chemother, 36(2), 484-485).

[0274] The efflux of 7-aminoheptanoate and heptamethylenediamine can be enhanced or amplified by overexpressing the solute transporters such as the lysE transporter from Corynebacterium glutamicum (Bellmann et al., 2001, Microbiology, 147, 1765-1774).

[0275] The efflux of pimelic acid can be enhanced or amplified by overexpressing a dicarboxylate transporter such as the SucE transporter from Corynebacterium glutamicum (Huhn et al., Appl. Microbiol. & Biotech., 89(2), 327-335).

Producing C7 Building Blocks Using a Recombinant Host

[0276] Typically, one or more C7 building blocks can be produced by providing a host microorganism and culturing the provided microorganism with a culture medium containing a suitable carbon source as described above. In general, the culture media and/or culture conditions can be such that the microorganisms grow to an adequate density and produce a C7 building block efficiently. For large-scale production processes, any method can be used such as those described elsewhere (Manual of Industrial Microbiology and Biotechnology, 2.sup.nd Edition, Editors: A. L. Demain and J. E. Davies, ASM Press; and Principles of Fermentation Technology, P. F. Stanbury and A. Whitaker, Pergamon). Briefly, a large tank (e.g., a 100 gallon, 200 gallon, 500 gallon, or more tank) containing an appropriate culture medium is inoculated with a particular microorganism. After inoculation, the microorganism is incubated to allow biomass to be produced. Once a desired biomass is reached, the broth containing the microorganisms can be transferred to a second tank. This second tank can be any size. For example, the second tank can be larger, smaller, or the same size as the first tank. Typically, the second tank is larger than the first such that additional culture medium can be added to the broth from the first tank. In addition, the culture medium within this second tank can be the same as, or different from, that used in the first tank.

[0277] Once transferred, the microorganisms can be incubated to allow for the production of a C7 building block. Once produced, any method can be used to isolate C7 building blocks. For example, C7 building blocks can be recovered selectively from the fermentation broth via adsorption processes. In the case of pimelic acid and 7-aminoheptanoic acid, the resulting eluate can be further concentrated via evaporation, crystallized via evaporative and/or cooling crystallization, and the crystals recovered via centrifugation. In the case of heptamethylenediamine and 1,7-heptanediol, distillation may be employed to achieve the desired product purity.

[0278] Accordingly, the methods provided herein can be performed in a recombinant host. In some embodiments, the methods provided herein can be performed in a recombinant host by fermentation. In some embodiments, the recombinant host is subjected to a cultivation strategy under aerobic, anaerobic or, micro-aerobic cultivation conditions. In some embodiments, the recombinant host is cultured under conditions of nutrient limitation such as phosphate, nitrogen and oxygen limitation. In some embodiments, the recombinant host is retained using a ceramic membrane to maintain a high cell density during fermentation.

[0279] In some embodiments, the principal carbon source fed to the fermentation derives from biological or non-biological feedstocks. In some embodiments, the biological feedstock is, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid, formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste. In some embodiments, the non-biological feedstock is, or derives from, natural gas, syngas, CO.sub.2/H.sub.2, methanol, ethanol, benzoate, non-volatile residue (NVR) caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

[0280] In some embodiments, the recombinant host is a prokaryote. In some embodiments, the prokaryote is from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia acidovorans, from the genus Bacillus such as Bacillus subtillis; from the genes Lactobacillus such as Lactobacillus delbrueckii; from the genus Lactococcus such as Lactococcus lactis; or from the genus Rhodococcus such as Rhodococcus equi.

[0281] In some embodiments, the recombinant host is a eukaryote. In some embodiments, the eukaryote is from the genus Aspergillus such as Aspergillus niger; from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; from the genus Yarrowia such as Yarrowia lipolytica, from the genus Issatchenkia such as Issathenkia orientalis, from the genus Debaryomyces such as Debaryomyces hansenii, from the genus Arxula such as Arxula adenoinivorans, or from the genus Kluyveromyces such as Kluyveromyces lactis.

[0282] In some embodiments, the recombinant host includes one or more of the following polypeptides having attenuated activity: polyhydroxyalkanoate synthase activity, acetyl-CoA thioesterase activity, acetyl-CoA specific .beta.-ketothiolase activity, phosphotransacetylase forming acetate activity, acetate kinase activity, lactate dehydrogenase activity, menaquinol-fumarate oxidoreductase activity, 2-oxoacid decarboxylase producing isobutanol, alcohol dehydrogenase activity forming ethanol, triose phosphate isomerase activity, pyruvate decarboxylase activity, glucose-6-phosphate isomerase activity, transhydrogenase activity dissipating the NADPH imbalance, glutamate dehydrogenase activity dissipating the NADPH imbalance, NADH/NADPH-utilizing glutamate dehydrogenase activity, pimeloyl-CoA dehydrogenase activity; acyl-CoA dehydrogenase activity accepting C7 building blocks and central precursors as substrates; glutaryl-CoA dehydrogenase activity; or pimeloyl-CoA synthetase activity.

[0283] In some embodiments, the recombinant host overexpresses one or more genes encoding a polypeptide having: acetyl-CoA synthetase activity; transketolase activity; puridine nucleotide transhydrogenase activity; formate dehydrogenase activity; glyceraldehyde-3P-dehydrogenase activity; malic enzyme activity; glucose-6-phosphate dehydrogenase activity; fructose 1,6 diphosphatase activity; L-alanine dehydrogenase activity; PEP carboxylase activity, pyruvate carboxylase activity; PEP carboxykinase activity; PEP synthase activity; L-glutamate dehydrogenase activity specific to the NADPH used to generate a co-factor imbalance; methanol dehydrogenase activity, formaldehyde dehydrogenase activity, lysine transporter activity; dicarboxylate transporter activity; S-adenosylmethionine synthetase activity; 3-phosphoglycerate dehydrogenase activity; 3-phosphoserine aminotransferase activity; phosphoserine phosphatase activity; or a multidrug transporter activity.

[0284] The present document further provides a recombinant host comprising at least one exogenous nucleic acid encoding having (i) .beta.-ketoacyl-[acp]synthase activity or .beta.-ketothiolase activity, (ii) 3-hydroxybutyryl-CoA dehydrogenase activity, and (iii) enoyl-CoA hydratase activity.

[0285] In some embodiments, the recombinant host further includes one or more exogenous polypeptides having homocitrate synthase, homocitrate dehydratase, homoaconitate hydratase, isohomocitrate dehydrogenase, 2-hydroxyglutarate dehydrogenase, glutaconate CoA-transferase, or 2-hydroxyglutaryl-CoA dehydratase activity.

[0286] In some embodiments, the recombinant host further includes one or more exogenous polypeptides having glutarate semialdehyde dehydrogenase, 4-hydroxy-2-oxoheptanedioate aldolase, 2-oxo-hept-3-ene-1,7-dioate hydratase, 2-enoate reductase, 2-hydroxyglutarate dehydrogenase, glutaconate CoA-transferase, or 2-hydroxyglutaryl-CoA dehydratase activity.

[0287] In some embodiments, the recombinant host further includes one or more exogenous polypeptides having thioesterase, aldehyde dehydrogenase, 7-oxoheptanoate dehydrogenase, 6-oxohexanoate dehydrogenase, glutaconate CoA-transferase, reversible succinyl-CoA ligase, acetylating aldehyde dehydrogenase, or carboxylate reductase activity, the host further producing pimelic acid or pimelate semialdehyde.

[0288] In some embodiments, the recombinant host further includes an exogenous polypeptide having .omega.-transaminase activity, the host further producing 7-aminoheptanoate.

[0289] In some embodiments, the recombinant host further includes one or more exogenous polypeptides having 4-hydroxybutyrate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 6-hydroxyhexanoate dehydrogenase, or alcohol dehydrogenase activity, the host further producing 7-hydroxyheptanoic acid.

[0290] In some embodiments, the recombinant host further includes one or more exogenous polypeptides having .omega.-transaminase, deacetylase, N-acetyl transferase, or alcohol dehydrogenase activity, the host further producing heptamethylenediamine.

[0291] In some embodiments, the recombinant host further includes one or more exogenous polypeptides having (a) carboxylate reductase activity enhanced by phosphopantetheinyl transferase activity, or (b) alcohol dehydrogenase activity, the host further producing 1,7-heptanediol.

[0292] The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES

Example 1

Enzyme Activity of Thioesterases Using Pimeloyl-CoA as a Substrate and Forming Pimelic Acid

[0293] A sequence encoding an N-terminal His tag was added to the tesB gene from Escherichia coli that encodes a thioesterase (SEQ ID NO: 21, see FIG. 9), such that an N-terminal HIS tagged thioesterase could be produced. The modified tesB gene was cloned into a pET15b expression vector under control of the T7 promoter. The expression vector was transformed into a BL21[DE3] E. coli host. The resulting recombinant E. coli strain was cultivated at 37.degree. C. in a 500 mL shake flask culture containing 50 mL Luria Broth (LB) media and antibiotic selection pressure, with shaking at 230 rpm. The culture was induced overnight at 17.degree. C. using 0.5 mM IPTG.

[0294] The pellet from the induced shake flask culture was harvested via centrifugation. The pellet was resuspended and lysed in Y-per.TM. solution (ThermoScientific, Rockford, Ill.). The cell debris was separated from the supernatant via centrifugation. The thioesterase was purified from the supernatant using Ni-affinity chromatography and the eluate was buffer exchanged and concentrated via ultrafiltration.

[0295] The enzyme activity assay was performed in triplicate in a buffer composed of 50 mM phosphate buffer (pH=7.4), 0.1 mM Ellman's reagent, and 667 .mu.M of pimeloyl-CoA (as substrate). The enzyme activity assay reaction was initiated by adding 0.8 .mu.M of the tesB gene product to the assay buffer containing the pimeloyl-CoA and incubating at 37.degree. C. for 20 minutes. The release of Coenzyme A was monitored by absorbance at 412 nm. The absorbance associated with the substrate only control, which contained boiled enzyme, was subtracted from the active enzyme assay absorbance and compared to the empty vector control. The gene product of tesB accepted pimeloyl-CoA as substrate as confirmed via relative spectrophotometry (see, FIG. 10) and synthesized pimelate as a reaction product.

Example 2

Enzyme Activity of .omega.-Transaminase Using Pimelate Semialdehyde as Substrate and Forming 7-Aminoheptanoate

[0296] A sequence encoding an N-terminal His-tag was added to the genes from Chromobacterium violaceum, Pseudomonas syringae, Rhodobacter sphaeroides, and Vibrio fluvialis encoding the .omega.-transaminases of SEQ ID NOs: 13, 15, 16, and 18, respectively (see, FIG. 9) such that N-terminal HIS tagged .omega.-transaminases could be produced. Each of the resulting modified genes was cloned into a pET21a expression vector under control of the T7 promoter and each expression vector was transformed into a BL21[DE3] E. coli host. The resulting recombinant E. coli strains were cultivated at 37.degree. C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16.degree. C. using 1 mM IPTG.

[0297] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

[0298] Enzyme activity assays in the reverse direction (i.e., 7-aminoheptanoate to pimelate semialdehyde) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 7-aminoheptanoate, 10 mM pyruvate and 100 .mu.M pyridoxyl 5' phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the .omega.-transaminase gene product or the empty vector control to the assay buffer containing the 7-aminoheptanoate and incubated at 25.degree. C. for 4 hours, with shaking at 250 rpm. The formation of L-alanine from pyruvate was quantified via RP-HPLC.

[0299] Each enzyme only control without 7-aminoheptanoate demonstrated low base line conversion of pyruvate to L-alanine See, FIG. 16. The gene product of SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 18 accepted 7-aminoheptanote as substrate as confirmed against the empty vector control. See, FIG. 17.

[0300] Enzyme activity in the forward direction (i.e., pimelate semialdehyde to 7-aminoheptanoate) was confirmed for the transaminases of SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 18. Enzyme activity assays were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM pimelate semialdehyde, 10 mM L-alanine and 100 .mu.M pyridoxyl 5' phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the .omega.-transaminase gene product or the empty vector control to the assay buffer containing the pimelate semialdehyde and incubated at 25.degree. C. for 4 hours, with shaking at 250 rpm. The formation of pyruvate was quantified via RP-HPLC.

[0301] The gene product of SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 18 accepted pimelate semialdehyde as substrate as confirmed against the empty vector control. See, FIG. 18. The reversibility of the .omega.-transaminase activity was confirmed, demonstrating that the .omega.-transaminases of SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 18 accepted pimelate semialdehyde as substrate and synthesized 7-aminoheptanoate as a reaction product.

Example 3

Enzyme Activity of Carboxylate Reductase Using Pimelate as Substrate and Forming Pimelate Semialdehyde

[0302] A sequence encoding a HIS-tag was added to the genes from Segniliparus rugosus and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 9 and 12, respectively (see FIG. 9), such that N-terminal HIS tagged carboxylate reductases could be produced. Each of the modified genes was cloned into a pET Duet expression vector along with a sfp gene encoding a HIS-tagged phosphopantetheine transferase from Bacillus subtilis, both under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli host and the resulting recombinant E. coli strains were cultivated at 37.degree. C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37.degree. C. using an auto-induction media.

[0303] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication, and the cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferases were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5), and concentrated via ultrafiltration.

[0304] Enzyme activity assays (i.e., from pimelate to pimelate semialdehyde) were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM pimelate, 10 mM MgCl.sub.2, 1 mM ATP and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase gene products or the empty vector control to the assay buffer containing the pimelate and then incubated at room temperature for 20 minutes. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without pimelate demonstrated low base line consumption of NADPH. See, FIG. 11.

[0305] The gene products of SEQ ID NO: 9 and SEQ ID NO: 12, enhanced by the gene product of sfp, accepted pimelate as substrate, as confirmed against the empty vector control (see FIG. 12), and synthesized pimelate semialdehyde.

Example 4

Enzyme Activity of Carboxylate Reductase Using 7-Hydroxyheptanoate as Substrate and Forming 7-Hydroxyheptanal

[0306] A sequence encoding a His-tag was added to the genes from Mycobacterium marinum, Mycobacterium smegmatis, Segniliparus rugosus, Mycobacterium smegmatis, Mycobacterium massiliense, and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 7 to 12--respectively (see, FIG. 9) such that N-terminal HIS tagged carboxylate reductases could be produced. Each of the modified genes was cloned into a pET Duet expression vector alongside a sfp gene encoding a His-tagged phosphopantetheine transferase from Bacillus subtilis, both under control of the T7 promoter.

[0307] Each expression vector was transformed into a BL21[DE3] E. coli host and the resulting recombinant E. coli strains were cultivated at 37.degree. C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37.degree. C. using an auto-induction media.

[0308] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferase were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5) and concentrated via ultrafiltration.

[0309] Enzyme activity (i.e., 7-hydroxyheptanoate to 7-hydroxyheptanal) assays were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM 7-hydroxyheptanoate, 10 mM MgCl.sub.2, 1 mM ATP, and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the 7-hydroxyheptanoate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without 7-hydroxyheptanoate demonstrated low base line consumption of NADPH. See, FIG. 11.

[0310] The gene products of SEQ ID NOs: 7 to 12, enhanced by the gene product of sfp, accepted 7-hydroxyheptanoate as substrate as confirmed against the empty vector control (see, FIG. 13), and synthesized 7-hydroxyheptanal.

Example 5

Enzyme Activity of .omega.-Transaminase for 7-Aminoheptanol, Forming 7-Oxoheptanol

[0311] A nucleotide sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas syringae and Rhodobacter sphaeroides genes encoding the .omega.-transaminases of SEQ ID NOs: 13, 15, and 16, respectively (see, FIG. 9) such that N-terminal HIS tagged .omega.-transaminases could be produced. The modified genes were cloned into a pET21a expression vector under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli host. Each resulting recombinant E. coli strain were cultivated at 37.degree. C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16.degree. C. using 1 mM IPTG.

[0312] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

[0313] Enzyme activity assays in the reverse direction (i.e., 7-aminoheptanol to 7-oxoheptanol) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 7-aminoheptanol, 10 mM pyruvate, and 100 .mu.M pyridoxyl 5' phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the .omega.-transaminase gene product or the empty vector control to the assay buffer containing the 7-aminoheptanol and then incubated at 25.degree. C. for 4 hours, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

[0314] Each enzyme only control without 7-aminoheptanol had low base line conversion of pyruvate to L-alanine See, FIG. 16.

[0315] The gene products of SEQ ID NOs: 13, 15, and 16 accepted 7-aminoheptanol as substrate as confirmed against the empty vector control (see FIG. 21) and synthesized 7-oxoheptanol as reaction product. Given the reversibility of the .omega.-transaminase activity (see Example 2), it can be concluded that the gene products of SEQ ID NOs.: 13, 15, and 16 accept 7-oxoheptanol as substrate and form 7-aminoheptanol.

Example 6

Enzyme Activity of .omega.-Transaminase Using Heptamethylenediamine as Substrate and Forming 7-Aminoheptanal

[0316] A sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae, Rhodobacter sphaeroides, Escherichia coli, and Vibrio fluvialis genes encoding the .omega.-transaminases of SEQ ID NOs: 13 to 18, respectively (see, FIG. 9) such that N-terminal HIS tagged .omega.-transaminases could be produced. The modified genes were cloned into a pET21a expression vector under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli host. Each resulting recombinant E. coli strain were cultivated at 37.degree. C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16.degree. C. using 1 mM IPTG.

[0317] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

[0318] Enzyme activity assays in the reverse direction (i.e., heptamethylenediamine to 7-aminoheptanal) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM heptamethylenediamine, 10 mM pyruvate, and 100 .mu.M pyridoxyl 5' phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the .omega.-transaminase gene product or the empty vector control to the assay buffer containing the heptamethylenediamine and then incubated at 25.degree. C. for 4 hours, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

[0319] Each enzyme only control without heptamethylenediamine had low base line conversion of pyruvate to L-alanine. See, FIG. 16.

[0320] The gene products of SEQ ID NOs: 13 to 18 accepted heptamethylenediamine as substrate as confirmed against the empty vector control (see, FIG. 19) and synthesized 7-aminoheptanal as reaction product. Given the reversibility of the .omega.-transaminase activity (see Example 2), it can be concluded that the gene products of SEQ ID NOs: 13 to 18 accept 7-aminoheptanal as substrate and form heptamethylenediamine.

Example 7

Enzyme Activity of Carboxylate Reductase for N7-Acetyl-7-Aminoheptanoate, Forming N7-Acetyl-7-Aminoheptanal

[0321] The activity of each of the N-terminal His-tagged carboxylate reductases of SEQ ID NOs: 8, 11, and 12 (see Example 4, and FIG. 9) for converting N7-acetyl-7-aminoheptanoate to N7-acetyl-7-aminoheptanal was assayed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM N7-acetyl-7-aminoheptanoate, 10 mM MgCl.sub.2, 1 mM ATP, and 1 mM NADPH. The assays were initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the N7-acetyl-7-aminoheptanoate then incubated at room temperature for 20 minutes. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without N7-acetyl-7-aminoheptanoate demonstrated low base line consumption of NADPH. See, FIG. 11.

[0322] The gene products of SEQ ID NOs: 8, 11, and 12 enhanced by the gene product of sfp, accepted N7-acetyl-7-aminoheptanoate as substrate as confirmed against the empty vector control (see, FIG. 14), and synthesized N7-acetyl-7-aminoheptanal.

Example 8

Enzyme Activity of .omega.-Transaminase Using N7-Acetyl-1,7-Diaminoheptane, and Forming N7-Acetyl-7-Aminoheptanal

[0323] The activity of the N-terminal His-tagged .omega.-transaminases of SEQ ID NOs: 13 to 18 (see, Example 6, and FIG. 9) for converting N7-acetyl-1,7-diaminoheptane to N7-acetyl-7-aminoheptanal was assayed using a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM N7-acetyl-1,7-diaminoheptane, 10 mM pyruvate and 100 .mu.M pyridoxyl 5' phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the .omega.-transaminase or the empty vector control to the assay buffer containing the N7-acetyl-1,7-diaminoheptane then incubated at 25.degree. C. for 4 hours, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

[0324] Each enzyme only control without N7-acetyl-1,7-diaminoheptane demonstrated low base line conversion of pyruvate to L-alanine. See, FIG. 16.

[0325] The gene product of SEQ ID NOs: 13 to 18 accepted N7-acetyl-1,7-diaminoheptane as substrate as confirmed against the empty vector control (see FIG. 20) and synthesized N7-acetyl-7-aminoheptanal as reaction product.

[0326] Given the reversibility of the .omega.-transaminase activity (see example 2), the gene products of SEQ ID NOs: 13 to 18 accept N7-acetyl-7-aminoheptanal as substrate forming N7-acetyl-1,7-diaminoheptane.

Example 9

Enzyme Activity of Carboxylate Reductase Using Pimelate Semialdehyde as Substrate and Forming Heptanedial

[0327] The N-terminal His-tagged carboxylate reductase of SEQ ID NO: 12 (see, Example 4 and FIG. 9) was assayed using pimelate semialdehyde as substrate. The enzyme activity assay was performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM pimelate semialdehyde, 10 mM MgCl.sub.2, 1 mM ATP and 1 mM NADPH. The enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the pimelate semialdehyde and then incubated at room temperature for 20 minutes. The consumption of NADPH was monitored by absorbance at 340 nm. The enzyme only control without pimelate semialdehyde demonstrated low base line consumption of NADPH. See, FIG. 11.

[0328] The gene product of SEQ ID NO: 12, enhanced by the gene product of sfp, accepted pimelate semialdehyde as substrate as confirmed against the empty vector control (see, FIG. 15) and synthesized heptanedial.

Example 10

Enzyme Activity of Pimeloyl-[acp]Methylester Methylesterase Using Pimeloyl-CoA Methyl Ester as Substrate and Forming Pimeloyl-CoA

[0329] A nucleotide sequence encoding a C-terminal His-tag was added to the gene from Escherichia coli encoding the pimeloyl-[acp]methylester methylesterase of SEQ ID NO: 6 (see, FIG. 9) such that a C-terminal HIS tagged pimeloyl-[acp]methyl ester methylesterase could be produced. The resulting modified gene was cloned into a pET28b+ expression vector under control of the T7 promoter and the expression vector was transformed into a BL21[DE3] E. coli host. The resulting recombinant E. coli strain was cultivated at 37.degree. C. in a 500 mL shake flask culture containing 100 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 18.degree. C. using 0.3 mM IPTG.

[0330] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation. The pimeloyl-[acp]methyl ester methylesterase was purified from the supernatant using Ni-affinity chromatography, buffer exchanged and concentrated into 20 mM HEPES buffer (pH=7.5) via ultrafiltration and stored at 4.degree. C.

[0331] Enzyme activity assays converting pimeloyl-CoA methyl ester to pimeloyl-CoA were performed in triplicate in a buffer composed of a final concentration of 25 mM Tris HCl buffer (pH=7.0) and 5 [mM] pimeloyl-CoA methyl ester. The enzyme activity assay reaction was initiated by adding pimeloyl-[acp]methyl ester methylesterase to a final concentration of 10 [.mu.M] to the assay buffer containing the pimeloyl-CoA methyl ester and incubated at 30.degree. C. for 1 hour, with shaking at 250 rpm. The formation of pimeloyl-CoA was quantified via LC-MS.

[0332] The substrate only control without enzyme demonstrated no conversion of the substrate pimeloyl-CoA methyl ester to pimeloyl-CoA. See, FIG. 22. The pimeloyl-[acp]methyl ester methylesterase of SEQ ID NO: 6 accepted pimeloyl-CoA methyl ester as substrate and synthesized pimeloyl-CoA as reaction product as confirmed via LC-MS. See, FIG. 22.

Example 11

Enzyme Activity of .beta.-Ketothiolases Using Glutaryl-CoA and Acetyl-CoA as Substrates and Forming 3-Ketopimeloyl-CoA

[0333] A nucleotide sequence encoding a N-terminal His-tag was added to the gene from Pseudomonas reinekei MT1, Pseudomonas putida, Burkholderia xenovorans, Arthrobacter sp., Burkholderia xenovorans, Geobacillus kaustophilus, Gordonia bronchialis, Citrobacter freundii, Burkholderia sp., Beijerinckia indica, Arthrobacter arilaitensis, Cupriavidus necator and Escherichia coli encoding the .beta.-ketothiolase of SEQ ID NOs: 28 to 40 (see, FIG. 9) such that a N-terminal HIS tagged .beta.-ketothiolase could be produced. The resulting modified gene was cloned into a pET15b expression vector under control of the T7 promoter and the expression vector was transformed into a BL21[DE3] E. coli host. The resulting recombinant E. coli strain was cultivated at 37.degree. C. in a 1 L shake flask culture containing 350 mL LB media and ampicilin antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 25.degree. C. using 1 mM IPTG.

[0334] The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation. The .beta.-ketothiolase was purified from the supernatant using Ni-affinity chromatography, buffer exchanged and concentrated into 50 mM potassium phosphate buffer (pH=6.8) via ultrafiltration.

[0335] Enzyme activity assays converting glutaryl-CoA and acetyl-CoA to 3-ketopimeloyl-CoA were performed in triplicate in a buffer composed of a final concentration of 50 mM potassium phosphate buffer (pH=6.8) and 1 mM glutaryl-CoA and 1 mM acetyl-CoA. The enzyme activity assay reaction was initiated by adding .beta.-ketothiolase to a final concentration of 7 [.mu.M] to the assay buffer containing the 1 mM glutaryl-CoA and 1 mM acetyl-CoA and incubated at 30.degree. C. for three hours, with gentle shaking. The formation of 3-ketopimeloyl-CoA was quantified via LC-MS.

[0336] The substrate only control without enzyme demonstrated no conversion of the substrate pimeloyl-CoA methyl ester to pimeloyl-CoA. See, FIG. 23. The .beta.-ketothiolase of SEQ ID NOs: 28 to 40 accepted glutaryl-CoA and acetyl-CoA as substrates and synthesized 3-ketopimeloyl-CoA as reaction product as confirmed via LC-MS against the empty vector control. See, FIG. 23.

OTHER EMBODIMENTS

[0337] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Sequence CWU 1

1

401368PRTMycobacterium marinum 1Met Pro Arg Glu Ile Arg Leu Pro Glu Ser Ser Val Val Val Arg Pro1 5 10 15 Ala Pro Met Glu Ser Ala Thr Tyr Ser Gln Ser Ser Arg Leu Gln Ala 20 25 30 Ala Gly Leu Ser Pro Ala Ile Thr Leu Phe Glu Lys Ala Ala Gln Thr 35 40 45 Val Pro Leu Pro Asp Ala Pro Gln Pro Val Val Ile Ala Asp Tyr Gly 50 55 60 Val Ala Thr Gly His Asn Ser Leu Lys Pro Met Met Ala Ala Ile Asn65 70 75 80 Ala Leu Arg Arg Arg Ile Arg Glu Asp Arg Ala Ile Met Val Ala His 85 90 95 Thr Asp Val Pro Asp Asn Asp Phe Thr Ala Leu Phe Arg Thr Leu Ala 100 105 110 Asp Asp Pro Asp Ser Tyr Leu His His Asp Ser Ala Ser Phe Ala Ser 115 120 125 Ala Val Gly Arg Ser Phe Tyr Thr Gln Ile Leu Pro Ser Asn Thr Val 130 135 140 Ser Leu Gly Trp Ser Ser Trp Ala Ile Gln Trp Leu Ser Arg Ile Pro145 150 155 160 Ala Gly Ala Pro Glu Leu Thr Asp His Val Gln Val Ala Tyr Ser Lys 165 170 175 Asp Glu Arg Ala Arg Ala Ala Tyr Ala His Gln Ala Ala Thr Asp Trp 180 185 190 Gln Asp Phe Leu Ala Phe Arg Gly Arg Glu Leu Cys Pro Gly Gly Arg 195 200 205 Leu Val Val Leu Thr Met Ala Leu Asp Glu His Gly His Phe Gly Tyr 210 215 220 Arg Pro Met Asn Asp Ala Leu Val Ala Ala Leu Asn Asp Gln Val Arg225 230 235 240 Asp Gly Leu Leu Arg Pro Glu Glu Leu Arg Arg Met Ala Ile Pro Val 245 250 255 Val Ala Arg Ala Glu Lys Asp Leu Arg Ala Pro Phe Ala Pro Arg Gly 260 265 270 Trp Phe Glu Gly Leu Thr Ile Glu Gln Leu Asp Val Phe Asn Ala Glu 275 280 285 Asp Arg Phe Trp Ala Ala Phe Gln Ser Asp Gly Asp Ala Glu Ser Phe 290 295 300 Gly Ala Gln Trp Ala Gly Phe Ala Arg Ala Ala Leu Phe Pro Thr Leu305 310 315 320 Ala Ala Ala Leu Asp Cys Gly Thr Gly Asp Pro Arg Ala Thr Ala Phe 325 330 335 Ile Glu Gln Leu Glu Ala Ser Val Ala Asp Arg Leu Ala Ser Gln Pro 340 345 350 Glu Pro Met Arg Ile Pro Leu Ala Ser Leu Val Leu Ala Lys Arg Ala 355 360 365 2360PRTMycobacterium smegmatis 2Met Pro Lys Phe Arg Val Ala Val Asp Pro Glu Pro Asp Asp Pro Thr1 5 10 15 Pro Lys Met Arg Ala Pro Arg Pro His Ala Ala Gly Leu Asn Ser Ala 20 25 30 Ile Ala Leu Leu Glu Glu Ala Ala Arg Thr Val Pro Leu Pro Glu Ala 35 40 45 Pro Tyr Pro Ile Val Ile Ala Asp Tyr Gly Val Gly Thr Gly Arg Asn 50 55 60 Ser Met Arg Pro Ile Ala Ala Ala Ile Ala Ala Leu Arg Gly Arg Thr65 70 75 80 Arg Pro Glu His Ser Val Leu Val Thr His Thr Asp Asn Ala Asp Asn 85 90 95 Asp Phe Thr Ala Val Phe Arg Gly Leu Ala Asp Asn Pro Asp Ser Tyr 100 105 110 Leu Arg Arg Asp Thr Ser Thr Tyr Pro Ser Ala Val Gly Arg Ser Phe 115 120 125 Tyr Thr Gln Ile Leu Pro Ser Lys Ser Val His Val Gly Trp Ser Ala 130 135 140 Trp Ala Ile Val Arg Val Gly Arg Met Pro Met Pro Val Pro Asp His145 150 155 160 Val Ala Ala Ser Phe Ser Gly Asp Pro Gln Val Val Ala Ala Tyr Ala 165 170 175 Arg Gln Ala Ala Phe Asp Trp His Glu Phe Val Ala Phe Arg Gly Arg 180 185 190 Glu Leu Ala Ser Gly Ala Gln Leu Val Val Leu Thr Ala Ala Leu Gly 195 200 205 Asp Asp Gly Asp Phe Gly Tyr Arg Pro Leu Phe Ala Ala Val Met Asp 210 215 220 Thr Leu Arg Glu Leu Thr Ala Asp Gly Val Leu Arg Gln Asp Glu Leu225 230 235 240 His Arg Met Ser Leu Pro Ile Val Gly Arg Arg Ala Asn Asp Phe Met 245 250 255 Ala Pro Phe Ala Pro Ser Gly Arg Phe Glu Arg Leu Ser Ile Ser His 260 265 270 Leu Glu Val Tyr Asp Ala Glu Asp Val Ile Tyr Ser Ser Tyr Gln Lys 275 280 285 Asp Arg Asp Thr Asp Val Phe Gly Leu Arg Trp Ala Asp Phe Cys Arg 290 295 300 Phe Thr Phe Phe Ser Asp Leu Cys Thr Ala Leu Asp Asp Asp Ala Ala305 310 315 320 Arg Cys Thr Gln Phe Gln Asp Arg Leu His Ala Gly Ile Ala Ala Arg 325 330 335 Leu Ser Ala Gln Pro Glu Gln Met Arg Ile Pro Leu Ala Gln Leu Val 340 345 350 Leu Glu Arg Arg Arg Arg Ser Gly 355 360 3394PRTPseudomonas putida 3Met Leu Ala Gln Leu Pro Pro Ala Leu Gln Ser Leu His Leu Pro Leu1 5 10 15 Arg Leu Lys Leu Trp Asp Gly Asn Gln Phe Asp Leu Gly Pro Ser Pro 20 25 30 Gln Val Thr Ile Leu Val Lys Glu Pro Gln Leu Ile Gly Gln Leu Thr 35 40 45 His Pro Ser Met Glu Gln Leu Gly Thr Ala Phe Val Glu Gly Lys Leu 50 55 60 Glu Leu Glu Gly Asp Ile Gly Glu Ala Ile Arg Val Cys Asp Glu Leu65 70 75 80 Ser Glu Ala Leu Phe Thr Asp Glu Asp Glu Gln Pro Pro Glu Arg Arg 85 90 95 Ser His Asp Lys Arg Thr Asp Ala Glu Ala Ile Ser Tyr His Tyr Asp 100 105 110 Val Ser Asn Ala Phe Tyr Gln Leu Trp Leu Asp Gln Asp Met Ala Tyr 115 120 125 Ser Cys Ala Tyr Phe Arg Glu Pro Asp Asn Thr Leu Asp Gln Ala Gln 130 135 140 Gln Asp Lys Phe Asp His Leu Cys Arg Lys Leu Arg Leu Asn Ala Gly145 150 155 160 Asp Tyr Leu Leu Asp Val Gly Cys Gly Trp Gly Gly Leu Ala Arg Phe 165 170 175 Ala Ala Arg Glu Tyr Asp Ala Lys Val Phe Gly Ile Thr Leu Ser Lys 180 185 190 Glu Gln Leu Lys Leu Gly Arg Gln Arg Val Lys Ala Glu Gly Leu Thr 195 200 205 Asp Lys Val Asp Leu Gln Ile Leu Asp Tyr Arg Asp Leu Pro Gln Asp 210 215 220 Gly Arg Phe Asp Lys Val Val Ser Val Gly Met Phe Glu His Val Gly225 230 235 240 His Ala Asn Leu Ala Leu Tyr Cys Gln Lys Leu Phe Gly Ala Val Arg 245 250 255 Glu Gly Gly Leu Val Met Asn His Gly Ile Thr Ala Lys His Val Asp 260 265 270 Gly Arg Pro Val Gly Arg Gly Ala Gly Glu Phe Ile Asp Arg Tyr Val 275 280 285 Phe Pro His Gly Glu Leu Pro His Leu Ser Met Ile Ser Ala Ser Ile 290 295 300 Cys Glu Ala Gly Leu Glu Val Val Asp Val Glu Ser Leu Arg Leu His305 310 315 320 Tyr Ala Lys Thr Leu His His Trp Ser Glu Asn Leu Glu Asn Gln Leu 325 330 335 His Lys Ala Ala Ala Leu Val Pro Glu Lys Thr Leu Arg Ile Trp Arg 340 345 350 Leu Tyr Leu Ala Gly Cys Ala Tyr Ala Phe Glu Lys Gly Trp Ile Asn 355 360 365 Leu His Gln Ile Leu Ala Val Lys Pro Tyr Ala Asp Gly His His Asp 370 375 380 Leu Pro Trp Thr Arg Glu Asp Met Tyr Arg385 390 4246PRTLactobacillus brevis 4Met Ala Ala Asn Glu Phe Ser Glu Thr His Arg Val Val Tyr Tyr Glu1 5 10 15 Ala Asp Asp Thr Gly Gln Leu Thr Leu Ala Met Leu Ile Asn Leu Phe 20 25 30 Val Leu Val Ser Glu Asp Gln Asn Asp Ala Leu Gly Leu Ser Thr Ala 35 40 45 Phe Val Gln Ser His Gly Val Gly Trp Val Val Thr Gln Tyr His Leu 50 55 60 His Ile Asp Glu Leu Pro Arg Thr Gly Ala Gln Val Thr Ile Lys Thr65 70 75 80 Arg Ala Thr Ala Tyr Asn Arg Tyr Phe Ala Tyr Arg Glu Tyr Trp Leu 85 90 95 Leu Asp Asp Ala Gly Gln Val Leu Ala Tyr Gly Glu Gly Ile Trp Val 100 105 110 Thr Met Ser Tyr Ala Thr Arg Lys Ile Thr Thr Ile Pro Ala Glu Val 115 120 125 Met Ala Pro Tyr His Ser Glu Glu Gln Thr Arg Leu Pro Arg Leu Pro 130 135 140 Arg Pro Asp His Phe Asp Glu Ala Val Asn Gln Thr Leu Lys Pro Tyr145 150 155 160 Thr Val Arg Tyr Phe Asp Ile Asp Gly Asn Gly His Val Asn Asn Ala 165 170 175 His Tyr Phe Asp Trp Met Leu Asp Val Leu Pro Ala Thr Phe Leu Arg 180 185 190 Ala His His Pro Thr Asp Val Lys Ile Arg Phe Glu Asn Glu Val Gln 195 200 205 Tyr Gly His Gln Val Thr Ser Glu Leu Ser Gln Ala Ala Ala Leu Thr 210 215 220 Thr Gln His Met Ile Lys Val Gly Asp Leu Thr Ala Val Lys Ala Thr225 230 235 240 Ile Gln Trp Asp Asn Arg 245 5261PRTLactobacillus plantarum 5Met Ala Thr Leu Gly Ala Asn Ala Ser Leu Tyr Ser Glu Gln His Arg1 5 10 15 Ile Thr Tyr Tyr Glu Cys Asp Arg Thr Gly Arg Ala Thr Leu Thr Thr 20 25 30 Leu Ile Asp Ile Ala Val Leu Ala Ser Glu Asp Gln Ser Asp Ala Leu 35 40 45 Gly Leu Thr Thr Glu Met Val Gln Ser His Gly Val Gly Trp Val Val 50 55 60 Thr Gln Tyr Ala Ile Asp Ile Thr Arg Met Pro Arg Gln Asp Glu Val65 70 75 80 Val Thr Ile Ala Val Arg Gly Ser Ala Tyr Asn Pro Tyr Phe Ala Tyr 85 90 95 Arg Glu Phe Trp Ile Arg Asp Ala Asp Gly Gln Gln Leu Ala Tyr Ile 100 105 110 Thr Ser Ile Trp Val Met Met Ser Gln Thr Thr Arg Arg Ile Val Lys 115 120 125 Ile Leu Pro Glu Leu Val Ala Pro Tyr Gln Ser Glu Val Val Lys Arg 130 135 140 Ile Pro Arg Leu Pro Arg Pro Ile Ser Phe Glu Ala Thr Asp Thr Thr145 150 155 160 Ile Thr Lys Pro Tyr His Val Arg Phe Phe Asp Ile Asp Pro Asn Arg 165 170 175 His Val Asn Asn Ala His Tyr Phe Asp Trp Leu Val Asp Thr Leu Pro 180 185 190 Ala Thr Phe Leu Leu Gln His Asp Leu Val His Val Asp Val Arg Tyr 195 200 205 Glu Asn Glu Val Lys Tyr Gly Gln Thr Val Thr Ala His Ala Asn Ile 210 215 220 Leu Pro Ser Glu Val Ala Asp Gln Val Thr Thr Ser His Leu Ile Glu225 230 235 240 Val Asp Asp Glu Lys Cys Cys Glu Val Thr Ile Gln Trp Arg Thr Leu 245 250 255 Pro Glu Pro Ile Gln 260 6256PRTEscherichia coli 6Met Asn Asn Ile Trp Trp Gln Thr Lys Gly Gln Gly Asn Val His Leu1 5 10 15 Val Leu Leu His Gly Trp Gly Leu Asn Ala Glu Val Trp Arg Cys Ile 20 25 30 Asp Glu Glu Leu Ser Ser His Phe Thr Leu His Leu Val Asp Leu Pro 35 40 45 Gly Phe Gly Arg Ser Arg Gly Phe Gly Ala Leu Ser Leu Ala Asp Met 50 55 60 Ala Glu Ala Val Leu Gln Gln Ala Pro Asp Lys Ala Ile Trp Leu Gly65 70 75 80 Trp Ser Leu Gly Gly Leu Val Ala Ser Gln Ile Ala Leu Thr His Pro 85 90 95 Glu Arg Val Gln Ala Leu Val Thr Val Ala Ser Ser Pro Cys Phe Ser 100 105 110 Ala Arg Asp Glu Trp Pro Gly Ile Lys Pro Asp Val Leu Ala Gly Phe 115 120 125 Gln Gln Gln Leu Ser Asp Asp Phe Gln Arg Thr Val Glu Arg Phe Leu 130 135 140 Ala Leu Gln Thr Met Gly Thr Glu Thr Ala Arg Gln Asp Ala Arg Ala145 150 155 160 Leu Lys Lys Thr Val Leu Ala Leu Pro Met Pro Glu Val Asp Val Leu 165 170 175 Asn Gly Gly Leu Glu Ile Leu Lys Thr Val Asp Leu Arg Gln Pro Leu 180 185 190 Gln Asn Val Ser Met Pro Phe Leu Arg Leu Tyr Gly Tyr Leu Asp Gly 195 200 205 Leu Val Pro Arg Lys Val Val Pro Met Leu Asp Lys Leu Trp Pro His 210 215 220 Ser Glu Ser Tyr Ile Phe Ala Lys Ala Ala His Ala Pro Phe Ile Ser225 230 235 240 His Pro Ala Glu Phe Cys His Leu Leu Val Ala Leu Lys Gln Arg Val 245 250 255 71174PRTMycobacterium marinum 7Met Ser Pro Ile Thr Arg Glu Glu Arg Leu Glu Arg Arg Ile Gln Asp1 5 10 15 Leu Tyr Ala Asn Asp Pro Gln Phe Ala Ala Ala Lys Pro Ala Thr Ala 20 25 30 Ile Thr Ala Ala Ile Glu Arg Pro Gly Leu Pro Leu Pro Gln Ile Ile 35 40 45 Glu Thr Val Met Thr Gly Tyr Ala Asp Arg Pro Ala Leu Ala Gln Arg 50 55 60 Ser Val Glu Phe Val Thr Asp Ala Gly Thr Gly His Thr Thr Leu Arg65 70 75 80 Leu Leu Pro His Phe Glu Thr Ile Ser Tyr Gly Glu Leu Trp Asp Arg 85 90 95 Ile Ser Ala Leu Ala Asp Val Leu Ser Thr Glu Gln Thr Val Lys Pro 100 105 110 Gly Asp Arg Val Cys Leu Leu Gly Phe Asn Ser Val Asp Tyr Ala Thr 115 120 125 Ile Asp Met Thr Leu Ala Arg Leu Gly Ala Val Ala Val Pro Leu Gln 130 135 140 Thr Ser Ala Ala Ile Thr Gln Leu Gln Pro Ile Val Ala Glu Thr Gln145 150 155 160 Pro Thr Met Ile Ala Ala Ser Val Asp Ala Leu Ala Asp Ala Thr Glu 165 170 175 Leu Ala Leu Ser Gly Gln Thr Ala Thr Arg Val Leu Val Phe Asp His 180 185 190 His Arg Gln Val Asp Ala His Arg Ala Ala Val Glu Ser Ala Arg Glu 195 200 205 Arg Leu Ala Gly Ser Ala Val Val Glu Thr Leu Ala Glu Ala Ile Ala 210 215 220 Arg Gly Asp Val Pro Arg Gly Ala Ser Ala Gly Ser Ala Pro Gly Thr225 230 235 240 Asp Val Ser Asp Asp Ser Leu Ala Leu Leu Ile Tyr Thr Ser Gly Ser 245 250 255 Thr Gly Ala Pro Lys Gly Ala Met Tyr Pro Arg Arg Asn Val Ala Thr 260 265 270 Phe Trp Arg Lys Arg Thr Trp Phe Glu Gly Gly Tyr Glu Pro Ser Ile 275 280 285 Thr Leu Asn Phe Met Pro Met Ser His Val Met Gly Arg Gln Ile Leu 290 295 300 Tyr Gly Thr Leu Cys Asn Gly Gly Thr Ala Tyr Phe Val Ala Lys Ser305 310 315 320 Asp Leu Ser Thr Leu Phe Glu Asp Leu Ala Leu Val Arg Pro Thr Glu 325 330 335 Leu Thr Phe Val Pro Arg Val Trp Asp Met Val Phe Asp Glu Phe Gln 340 345 350 Ser Glu Val Asp Arg Arg Leu Val Asp Gly Ala Asp Arg Val Ala Leu 355 360 365 Glu Ala Gln Val Lys Ala Glu Ile Arg Asn Asp Val Leu Gly Gly Arg 370 375 380 Tyr Thr Ser Ala Leu Thr Gly Ser Ala Pro Ile Ser Asp Glu Met Lys385 390 395 400 Ala Trp Val Glu Glu

Leu Leu Asp Met His Leu Val Glu Gly Tyr Gly 405 410 415 Ser Thr Glu Ala Gly Met Ile Leu Ile Asp Gly Ala Ile Arg Arg Pro 420 425 430 Ala Val Leu Asp Tyr Lys Leu Val Asp Val Pro Asp Leu Gly Tyr Phe 435 440 445 Leu Thr Asp Arg Pro His Pro Arg Gly Glu Leu Leu Val Lys Thr Asp 450 455 460 Ser Leu Phe Pro Gly Tyr Tyr Gln Arg Ala Glu Val Thr Ala Asp Val465 470 475 480 Phe Asp Ala Asp Gly Phe Tyr Arg Thr Gly Asp Ile Met Ala Glu Val 485 490 495 Gly Pro Glu Gln Phe Val Tyr Leu Asp Arg Arg Asn Asn Val Leu Lys 500 505 510 Leu Ser Gln Gly Glu Phe Val Thr Val Ser Lys Leu Glu Ala Val Phe 515 520 525 Gly Asp Ser Pro Leu Val Arg Gln Ile Tyr Ile Tyr Gly Asn Ser Ala 530 535 540 Arg Ala Tyr Leu Leu Ala Val Ile Val Pro Thr Gln Glu Ala Leu Asp545 550 555 560 Ala Val Pro Val Glu Glu Leu Lys Ala Arg Leu Gly Asp Ser Leu Gln 565 570 575 Glu Val Ala Lys Ala Ala Gly Leu Gln Ser Tyr Glu Ile Pro Arg Asp 580 585 590 Phe Ile Ile Glu Thr Thr Pro Trp Thr Leu Glu Asn Gly Leu Leu Thr 595 600 605 Gly Ile Arg Lys Leu Ala Arg Pro Gln Leu Lys Lys His Tyr Gly Glu 610 615 620 Leu Leu Glu Gln Ile Tyr Thr Asp Leu Ala His Gly Gln Ala Asp Glu625 630 635 640 Leu Arg Ser Leu Arg Gln Ser Gly Ala Asp Ala Pro Val Leu Val Thr 645 650 655 Val Cys Arg Ala Ala Ala Ala Leu Leu Gly Gly Ser Ala Ser Asp Val 660 665 670 Gln Pro Asp Ala His Phe Thr Asp Leu Gly Gly Asp Ser Leu Ser Ala 675 680 685 Leu Ser Phe Thr Asn Leu Leu His Glu Ile Phe Asp Ile Glu Val Pro 690 695 700 Val Gly Val Ile Val Ser Pro Ala Asn Asp Leu Gln Ala Leu Ala Asp705 710 715 720 Tyr Val Glu Ala Ala Arg Lys Pro Gly Ser Ser Arg Pro Thr Phe Ala 725 730 735 Ser Val His Gly Ala Ser Asn Gly Gln Val Thr Glu Val His Ala Gly 740 745 750 Asp Leu Ser Leu Asp Lys Phe Ile Asp Ala Ala Thr Leu Ala Glu Ala 755 760 765 Pro Arg Leu Pro Ala Ala Asn Thr Gln Val Arg Thr Val Leu Leu Thr 770 775 780 Gly Ala Thr Gly Phe Leu Gly Arg Tyr Leu Ala Leu Glu Trp Leu Glu785 790 795 800 Arg Met Asp Leu Val Asp Gly Lys Leu Ile Cys Leu Val Arg Ala Lys 805 810 815 Ser Asp Thr Glu Ala Arg Ala Arg Leu Asp Lys Thr Phe Asp Ser Gly 820 825 830 Asp Pro Glu Leu Leu Ala His Tyr Arg Ala Leu Ala Gly Asp His Leu 835 840 845 Glu Val Leu Ala Gly Asp Lys Gly Glu Ala Asp Leu Gly Leu Asp Arg 850 855 860 Gln Thr Trp Gln Arg Leu Ala Asp Thr Val Asp Leu Ile Val Asp Pro865 870 875 880 Ala Ala Leu Val Asn His Val Leu Pro Tyr Ser Gln Leu Phe Gly Pro 885 890 895 Asn Ala Leu Gly Thr Ala Glu Leu Leu Arg Leu Ala Leu Thr Ser Lys 900 905 910 Ile Lys Pro Tyr Ser Tyr Thr Ser Thr Ile Gly Val Ala Asp Gln Ile 915 920 925 Pro Pro Ser Ala Phe Thr Glu Asp Ala Asp Ile Arg Val Ile Ser Ala 930 935 940 Thr Arg Ala Val Asp Asp Ser Tyr Ala Asn Gly Tyr Ser Asn Ser Lys945 950 955 960 Trp Ala Gly Glu Val Leu Leu Arg Glu Ala His Asp Leu Cys Gly Leu 965 970 975 Pro Val Ala Val Phe Arg Cys Asp Met Ile Leu Ala Asp Thr Thr Trp 980 985 990 Ala Gly Gln Leu Asn Val Pro Asp Met Phe Thr Arg Met Ile Leu Ser 995 1000 1005 Leu Ala Ala Thr Gly Ile Ala Pro Gly Ser Phe Tyr Glu Leu Ala Ala 1010 1015 1020 Asp Gly Ala Arg Gln Arg Ala His Tyr Asp Gly Leu Pro Val Glu Phe1025 1030 1035 1040 Ile Ala Glu Ala Ile Ser Thr Leu Gly Ala Gln Ser Gln Asp Gly Phe 1045 1050 1055 His Thr Tyr His Val Met Asn Pro Tyr Asp Asp Gly Ile Gly Leu Asp 1060 1065 1070 Glu Phe Val Asp Trp Leu Asn Glu Ser Gly Cys Pro Ile Gln Arg Ile 1075 1080 1085 Ala Asp Tyr Gly Asp Trp Leu Gln Arg Phe Glu Thr Ala Leu Arg Ala 1090 1095 1100 Leu Pro Asp Arg Gln Arg His Ser Ser Leu Leu Pro Leu Leu His Asn1105 1110 1115 1120 Tyr Arg Gln Pro Glu Arg Pro Val Arg Gly Ser Ile Ala Pro Thr Asp 1125 1130 1135 Arg Phe Arg Ala Ala Val Gln Glu Ala Lys Ile Gly Pro Asp Lys Asp 1140 1145 1150 Ile Pro His Val Gly Ala Pro Ile Ile Val Lys Tyr Val Ser Asp Leu 1155 1160 1165 Arg Leu Leu Gly Leu Leu 1170 81173PRTMycobacterium smegmatis 8Met Thr Ser Asp Val His Asp Ala Thr Asp Gly Val Thr Glu Thr Ala1 5 10 15 Leu Asp Asp Glu Gln Ser Thr Arg Arg Ile Ala Glu Leu Tyr Ala Thr 20 25 30 Asp Pro Glu Phe Ala Ala Ala Ala Pro Leu Pro Ala Val Val Asp Ala 35 40 45 Ala His Lys Pro Gly Leu Arg Leu Ala Glu Ile Leu Gln Thr Leu Phe 50 55 60 Thr Gly Tyr Gly Asp Arg Pro Ala Leu Gly Tyr Arg Ala Arg Glu Leu65 70 75 80 Ala Thr Asp Glu Gly Gly Arg Thr Val Thr Arg Leu Leu Pro Arg Phe 85 90 95 Asp Thr Leu Thr Tyr Ala Gln Val Trp Ser Arg Val Gln Ala Val Ala 100 105 110 Ala Ala Leu Arg His Asn Phe Ala Gln Pro Ile Tyr Pro Gly Asp Ala 115 120 125 Val Ala Thr Ile Gly Phe Ala Ser Pro Asp Tyr Leu Thr Leu Asp Leu 130 135 140 Val Cys Ala Tyr Leu Gly Leu Val Ser Val Pro Leu Gln His Asn Ala145 150 155 160 Pro Val Ser Arg Leu Ala Pro Ile Leu Ala Glu Val Glu Pro Arg Ile 165 170 175 Leu Thr Val Ser Ala Glu Tyr Leu Asp Leu Ala Val Glu Ser Val Arg 180 185 190 Asp Val Asn Ser Val Ser Gln Leu Val Val Phe Asp His His Pro Glu 195 200 205 Val Asp Asp His Arg Asp Ala Leu Ala Arg Ala Arg Glu Gln Leu Ala 210 215 220 Gly Lys Gly Ile Ala Val Thr Thr Leu Asp Ala Ile Ala Asp Glu Gly225 230 235 240 Ala Gly Leu Pro Ala Glu Pro Ile Tyr Thr Ala Asp His Asp Gln Arg 245 250 255 Leu Ala Met Ile Leu Tyr Thr Ser Gly Ser Thr Gly Ala Pro Lys Gly 260 265 270 Ala Met Tyr Thr Glu Ala Met Val Ala Arg Leu Trp Thr Met Ser Phe 275 280 285 Ile Thr Gly Asp Pro Thr Pro Val Ile Asn Val Asn Phe Met Pro Leu 290 295 300 Asn His Leu Gly Gly Arg Ile Pro Ile Ser Thr Ala Val Gln Asn Gly305 310 315 320 Gly Thr Ser Tyr Phe Val Pro Glu Ser Asp Met Ser Thr Leu Phe Glu 325 330 335 Asp Leu Ala Leu Val Arg Pro Thr Glu Leu Gly Leu Val Pro Arg Val 340 345 350 Ala Asp Met Leu Tyr Gln His His Leu Ala Thr Val Asp Arg Leu Val 355 360 365 Thr Gln Gly Ala Asp Glu Leu Thr Ala Glu Lys Gln Ala Gly Ala Glu 370 375 380 Leu Arg Glu Gln Val Leu Gly Gly Arg Val Ile Thr Gly Phe Val Ser385 390 395 400 Thr Ala Pro Leu Ala Ala Glu Met Arg Ala Phe Leu Asp Ile Thr Leu 405 410 415 Gly Ala His Ile Val Asp Gly Tyr Gly Leu Thr Glu Thr Gly Ala Val 420 425 430 Thr Arg Asp Gly Val Ile Val Arg Pro Pro Val Ile Asp Tyr Lys Leu 435 440 445 Ile Asp Val Pro Glu Leu Gly Tyr Phe Ser Thr Asp Lys Pro Tyr Pro 450 455 460 Arg Gly Glu Leu Leu Val Arg Ser Gln Thr Leu Thr Pro Gly Tyr Tyr465 470 475 480 Lys Arg Pro Glu Val Thr Ala Ser Val Phe Asp Arg Asp Gly Tyr Tyr 485 490 495 His Thr Gly Asp Val Met Ala Glu Thr Ala Pro Asp His Leu Val Tyr 500 505 510 Val Asp Arg Arg Asn Asn Val Leu Lys Leu Ala Gln Gly Glu Phe Val 515 520 525 Ala Val Ala Asn Leu Glu Ala Val Phe Ser Gly Ala Ala Leu Val Arg 530 535 540 Gln Ile Phe Val Tyr Gly Asn Ser Glu Arg Ser Phe Leu Leu Ala Val545 550 555 560 Val Val Pro Thr Pro Glu Ala Leu Glu Gln Tyr Asp Pro Ala Ala Leu 565 570 575 Lys Ala Ala Leu Ala Asp Ser Leu Gln Arg Thr Ala Arg Asp Ala Glu 580 585 590 Leu Gln Ser Tyr Glu Val Pro Ala Asp Phe Ile Val Glu Thr Glu Pro 595 600 605 Phe Ser Ala Ala Asn Gly Leu Leu Ser Gly Val Gly Lys Leu Leu Arg 610 615 620 Pro Asn Leu Lys Asp Arg Tyr Gly Gln Arg Leu Glu Gln Met Tyr Ala625 630 635 640 Asp Ile Ala Ala Thr Gln Ala Asn Gln Leu Arg Glu Leu Arg Arg Ala 645 650 655 Ala Ala Thr Gln Pro Val Ile Asp Thr Leu Thr Gln Ala Ala Ala Thr 660 665 670 Ile Leu Gly Thr Gly Ser Glu Val Ala Ser Asp Ala His Phe Thr Asp 675 680 685 Leu Gly Gly Asp Ser Leu Ser Ala Leu Thr Leu Ser Asn Leu Leu Ser 690 695 700 Asp Phe Phe Gly Phe Glu Val Pro Val Gly Thr Ile Val Asn Pro Ala705 710 715 720 Thr Asn Leu Ala Gln Leu Ala Gln His Ile Glu Ala Gln Arg Thr Ala 725 730 735 Gly Asp Arg Arg Pro Ser Phe Thr Thr Val His Gly Ala Asp Ala Thr 740 745 750 Glu Ile Arg Ala Ser Glu Leu Thr Leu Asp Lys Phe Ile Asp Ala Glu 755 760 765 Thr Leu Arg Ala Ala Pro Gly Leu Pro Lys Val Thr Thr Glu Pro Arg 770 775 780 Thr Val Leu Leu Ser Gly Ala Asn Gly Trp Leu Gly Arg Phe Leu Thr785 790 795 800 Leu Gln Trp Leu Glu Arg Leu Ala Pro Val Gly Gly Thr Leu Ile Thr 805 810 815 Ile Val Arg Gly Arg Asp Asp Ala Ala Ala Arg Ala Arg Leu Thr Gln 820 825 830 Ala Tyr Asp Thr Asp Pro Glu Leu Ser Arg Arg Phe Ala Glu Leu Ala 835 840 845 Asp Arg His Leu Arg Val Val Ala Gly Asp Ile Gly Asp Pro Asn Leu 850 855 860 Gly Leu Thr Pro Glu Ile Trp His Arg Leu Ala Ala Glu Val Asp Leu865 870 875 880 Val Val His Pro Ala Ala Leu Val Asn His Val Leu Pro Tyr Arg Gln 885 890 895 Leu Phe Gly Pro Asn Val Val Gly Thr Ala Glu Val Ile Lys Leu Ala 900 905 910 Leu Thr Glu Arg Ile Lys Pro Val Thr Tyr Leu Ser Thr Val Ser Val 915 920 925 Ala Met Gly Ile Pro Asp Phe Glu Glu Asp Gly Asp Ile Arg Thr Val 930 935 940 Ser Pro Val Arg Pro Leu Asp Gly Gly Tyr Ala Asn Gly Tyr Gly Asn945 950 955 960 Ser Lys Trp Ala Gly Glu Val Leu Leu Arg Glu Ala His Asp Leu Cys 965 970 975 Gly Leu Pro Val Ala Thr Phe Arg Ser Asp Met Ile Leu Ala His Pro 980 985 990 Arg Tyr Arg Gly Gln Val Asn Val Pro Asp Met Phe Thr Arg Leu Leu 995 1000 1005 Leu Ser Leu Leu Ile Thr Gly Val Ala Pro Arg Ser Phe Tyr Ile Gly 1010 1015 1020 Asp Gly Glu Arg Pro Arg Ala His Tyr Pro Gly Leu Thr Val Asp Phe1025 1030 1035 1040 Val Ala Glu Ala Val Thr Thr Leu Gly Ala Gln Gln Arg Glu Gly Tyr 1045 1050 1055 Val Ser Tyr Asp Val Met Asn Pro His Asp Asp Gly Ile Ser Leu Asp 1060 1065 1070 Val Phe Val Asp Trp Leu Ile Arg Ala Gly His Pro Ile Asp Arg Val 1075 1080 1085 Asp Asp Tyr Asp Asp Trp Val Arg Arg Phe Glu Thr Ala Leu Thr Ala 1090 1095 1100 Leu Pro Glu Lys Arg Arg Ala Gln Thr Val Leu Pro Leu Leu His Ala1105 1110 1115 1120 Phe Arg Ala Pro Gln Ala Pro Leu Arg Gly Ala Pro Glu Pro Thr Glu 1125 1130 1135 Val Phe His Ala Ala Val Arg Thr Ala Lys Val Gly Pro Gly Asp Ile 1140 1145 1150 Pro His Leu Asp Glu Ala Leu Ile Asp Lys Tyr Ile Arg Asp Leu Arg 1155 1160 1165 Glu Phe Gly Leu Ile 1170 91148PRTSegniliparus rugosus 9 Met Gly Asp Gly Glu Glu Arg Ala Lys Arg Phe Phe Gln Arg Ile Gly1 5 10 15 Glu Leu Ser Ala Thr Asp Pro Gln Phe Ala Ala Ala Ala Pro Asp Pro 20 25 30 Ala Val Val Glu Ala Val Ser Asp Pro Ser Leu Ser Phe Thr Arg Tyr 35 40 45 Leu Asp Thr Leu Met Arg Gly Tyr Ala Glu Arg Pro Ala Leu Ala His 50 55 60 Arg Val Gly Ala Gly Tyr Glu Thr Ile Ser Tyr Gly Glu Leu Trp Ala65 70 75 80 Arg Val Gly Ala Ile Ala Ala Ala Trp Gln Ala Asp Gly Leu Ala Pro 85 90 95 Gly Asp Phe Val Ala Thr Val Gly Phe Thr Ser Pro Asp Tyr Val Ala 100 105 110 Val Asp Leu Ala Ala Ala Arg Ser Gly Leu Val Ser Val Pro Leu Gln 115 120 125 Ala Gly Ala Ser Leu Ala Gln Leu Val Gly Ile Leu Glu Glu Thr Glu 130 135 140 Pro Lys Val Leu Ala Ala Ser Ala Ser Ser Leu Glu Gly Ala Val Ala145 150 155 160 Cys Ala Leu Ala Ala Pro Ser Val Gln Arg Leu Val Val Phe Asp Leu 165 170 175 Arg Gly Pro Asp Ala Ser Glu Ser Ala Ala Asp Glu Arg Arg Gly Ala 180 185 190 Leu Ala Asp Ala Glu Glu Gln Leu Ala Arg Ala Gly Arg Ala Val Val 195 200 205 Val Glu Thr Leu Ala Asp Leu Ala Ala Arg Gly Glu Ala Leu Pro Glu 210 215 220 Ala Pro Leu Phe Glu Pro Ala Glu Gly Glu Asp Pro Leu Ala Leu Leu225 230 235 240 Ile Tyr Thr Ser Gly Ser Thr Gly Ala Pro Lys Gly Ala Met Tyr Ser 245 250 255 Gln Arg Leu Val Ser Gln Leu Trp Gly Arg Thr Pro Val Val Pro Gly 260 265 270 Met Pro Asn Ile Ser Leu His Tyr Met Pro Leu Ser His Ser Tyr Gly 275 280 285 Arg Ala Val Leu Ala Gly Ala Leu Ser Ala Gly Gly Thr Ala His Phe 290 295 300 Thr Ala Asn Ser Asp Leu Ser Thr Leu Phe Glu Asp Ile Ala Leu Ala305 310 315 320 Arg Pro Thr Phe Leu Ala Leu Val Pro Arg Val Cys Glu Met Leu Phe 325 330 335 Gln Glu Ser Gln Arg Gly Gln Asp Val Ala Glu Leu Arg Glu Arg Val 340 345 350 Leu Gly Gly Arg Leu Leu Val Ala Val Cys Gly Ser Ala Pro Leu

Ser 355 360 365 Pro Glu Met Arg Ala Phe Met Glu Glu Val Leu Gly Phe Pro Leu Leu 370 375 380 Asp Gly Tyr Gly Ser Thr Glu Ala Leu Gly Val Met Arg Asn Gly Ile385 390 395 400 Ile Gln Arg Pro Pro Val Ile Asp Tyr Lys Leu Val Asp Val Pro Glu 405 410 415 Leu Gly Tyr Arg Thr Thr Asp Lys Pro Tyr Pro Arg Gly Glu Leu Cys 420 425 430 Ile Arg Ser Thr Ser Leu Ile Ser Gly Tyr Tyr Lys Arg Pro Glu Ile 435 440 445 Thr Ala Glu Val Phe Asp Ala Gln Gly Tyr Tyr Lys Thr Gly Asp Val 450 455 460 Met Ala Glu Ile Ala Pro Asp His Leu Val Tyr Val Asp Arg Ser Lys465 470 475 480 Asn Val Leu Lys Leu Ser Gln Gly Glu Phe Val Ala Val Ala Lys Leu 485 490 495 Glu Ala Ala Tyr Gly Thr Ser Pro Tyr Val Lys Gln Ile Phe Val Tyr 500 505 510 Gly Asn Ser Glu Arg Ser Phe Leu Leu Ala Val Val Val Pro Asn Ala 515 520 525 Glu Val Leu Gly Ala Arg Asp Gln Glu Glu Ala Lys Pro Leu Ile Ala 530 535 540 Ala Ser Leu Gln Lys Ile Ala Lys Glu Ala Gly Leu Gln Ser Tyr Glu545 550 555 560 Val Pro Arg Asp Phe Leu Ile Glu Thr Glu Pro Phe Thr Thr Gln Asn 565 570 575 Gly Leu Leu Ser Glu Val Gly Lys Leu Leu Arg Pro Lys Leu Lys Ala 580 585 590 Arg Tyr Gly Glu Ala Leu Glu Ala Arg Tyr Asp Glu Ile Ala His Gly 595 600 605 Gln Ala Asp Glu Leu Arg Ala Leu Arg Asp Gly Ala Gly Gln Arg Pro 610 615 620 Val Val Glu Thr Val Val Arg Ala Ala Val Ala Ile Ser Gly Ser Glu625 630 635 640 Gly Ala Glu Val Gly Pro Glu Ala Asn Phe Ala Asp Leu Gly Gly Asp 645 650 655 Ser Leu Ser Ala Leu Ser Leu Ala Asn Leu Leu His Asp Val Phe Glu 660 665 670 Val Glu Val Pro Val Arg Ile Ile Ile Gly Pro Thr Ala Ser Leu Ala 675 680 685 Gly Ile Ala Lys His Ile Glu Ala Glu Arg Ala Gly Ala Ser Ala Pro 690 695 700 Thr Ala Ala Ser Val His Gly Ala Gly Ala Thr Arg Ile Arg Ala Ser705 710 715 720 Glu Leu Thr Leu Glu Lys Phe Leu Pro Glu Asp Leu Leu Ala Ala Ala 725 730 735 Lys Gly Leu Pro Ala Ala Asp Gln Val Arg Thr Val Leu Leu Thr Gly 740 745 750 Ala Asn Gly Trp Leu Gly Arg Phe Leu Ala Leu Glu Gln Leu Glu Arg 755 760 765 Leu Ala Arg Ser Gly Gln Asp Gly Gly Lys Leu Ile Cys Leu Val Arg 770 775 780 Gly Lys Asp Ala Ala Ala Ala Arg Arg Arg Ile Glu Glu Thr Leu Gly785 790 795 800 Thr Asp Pro Ala Leu Ala Ala Arg Phe Ala Glu Leu Ala Glu Gly Arg 805 810 815 Leu Glu Val Val Pro Gly Asp Val Gly Glu Pro Lys Phe Gly Leu Asp 820 825 830 Asp Ala Ala Trp Asp Arg Leu Ala Glu Glu Val Asp Val Ile Val His 835 840 845 Pro Ala Ala Leu Val Asn His Val Leu Pro Tyr His Gln Leu Phe Gly 850 855 860 Pro Asn Val Val Gly Thr Ala Glu Ile Ile Arg Leu Ala Ile Thr Ala865 870 875 880 Lys Arg Lys Pro Val Thr Tyr Leu Ser Thr Val Ala Val Ala Ala Gly 885 890 895 Val Glu Pro Ser Ser Phe Glu Glu Asp Gly Asp Ile Arg Ala Val Val 900 905 910 Pro Glu Arg Pro Leu Gly Asp Gly Tyr Ala Asn Gly Tyr Gly Asn Ser 915 920 925 Lys Trp Ala Gly Glu Val Leu Leu Arg Glu Ala His Glu Leu Val Gly 930 935 940 Leu Pro Val Ala Val Phe Arg Ser Asp Met Ile Leu Ala His Thr Arg945 950 955 960 Tyr Thr Gly Gln Leu Asn Val Pro Asp Gln Phe Thr Arg Leu Val Leu 965 970 975 Ser Leu Leu Ala Thr Gly Ile Ala Pro Lys Ser Phe Tyr Gln Gln Gly 980 985 990 Ala Ala Gly Glu Arg Gln Arg Ala His Tyr Asp Gly Ile Pro Val Asp 995 1000 1005 Phe Thr Ala Glu Ala Ile Thr Thr Leu Gly Ala Glu Pro Ser Trp Phe 1010 1015 1020 Asp Gly Gly Ala Gly Phe Arg Ser Phe Asp Val Phe Asn Pro His His1025 1030 1035 1040 Asp Gly Val Gly Leu Asp Glu Phe Val Asp Trp Leu Ile Glu Ala Gly 1045 1050 1055 His Pro Ile Ser Arg Ile Asp Asp His Lys Glu Trp Phe Ala Arg Phe 1060 1065 1070 Glu Thr Ala Val Arg Gly Leu Pro Glu Ala Gln Arg Gln His Ser Leu 1075 1080 1085 Leu Pro Leu Leu Arg Ala Tyr Ser Phe Pro His Pro Pro Val Asp Gly 1090 1095 1100 Ser Val Tyr Pro Thr Gly Lys Phe Gln Gly Ala Val Lys Ala Ala Gln1105 1110 1115 1120 Val Gly Ser Asp His Asp Val Pro His Leu Gly Lys Ala Leu Ile Val 1125 1130 1135 Lys Tyr Ala Asp Asp Leu Lys Ala Leu Gly Leu Leu 1140 1145 101168PRTMycobacterium smegmatis 10Met Thr Ile Glu Thr Arg Glu Asp Arg Phe Asn Arg Arg Ile Asp His1 5 10 15 Leu Phe Glu Thr Asp Pro Gln Phe Ala Ala Ala Arg Pro Asp Glu Ala 20 25 30 Ile Ser Ala Ala Ala Ala Asp Pro Glu Leu Arg Leu Pro Ala Ala Val 35 40 45 Lys Gln Ile Leu Ala Gly Tyr Ala Asp Arg Pro Ala Leu Gly Lys Arg 50 55 60 Ala Val Glu Phe Val Thr Asp Glu Glu Gly Arg Thr Thr Ala Lys Leu65 70 75 80 Leu Pro Arg Phe Asp Thr Ile Thr Tyr Arg Gln Leu Ala Gly Arg Ile 85 90 95 Gln Ala Val Thr Asn Ala Trp His Asn His Pro Val Asn Ala Gly Asp 100 105 110 Arg Val Ala Ile Leu Gly Phe Thr Ser Val Asp Tyr Thr Thr Ile Asp 115 120 125 Ile Ala Leu Leu Glu Leu Gly Ala Val Ser Val Pro Leu Gln Thr Ser 130 135 140 Ala Pro Val Ala Gln Leu Gln Pro Ile Val Ala Glu Thr Glu Pro Lys145 150 155 160 Val Ile Ala Ser Ser Val Asp Phe Leu Ala Asp Ala Val Ala Leu Val 165 170 175 Glu Ser Gly Pro Ala Pro Ser Arg Leu Val Val Phe Asp Tyr Ser His 180 185 190 Glu Val Asp Asp Gln Arg Glu Ala Phe Glu Ala Ala Lys Gly Lys Leu 195 200 205 Ala Gly Thr Gly Val Val Val Glu Thr Ile Thr Asp Ala Leu Asp Arg 210 215 220 Gly Arg Ser Leu Ala Asp Ala Pro Leu Tyr Val Pro Asp Glu Ala Asp225 230 235 240 Pro Leu Thr Leu Leu Ile Tyr Thr Ser Gly Ser Thr Gly Thr Pro Lys 245 250 255 Gly Ala Met Tyr Pro Glu Ser Lys Thr Ala Thr Met Trp Gln Ala Gly 260 265 270 Ser Lys Ala Arg Trp Asp Glu Thr Leu Gly Val Met Pro Ser Ile Thr 275 280 285 Leu Asn Phe Met Pro Met Ser His Val Met Gly Arg Gly Ile Leu Cys 290 295 300 Ser Thr Leu Ala Ser Gly Gly Thr Ala Tyr Phe Ala Ala Arg Ser Asp305 310 315 320 Leu Ser Thr Phe Leu Glu Asp Leu Ala Leu Val Arg Pro Thr Gln Leu 325 330 335 Asn Phe Val Pro Arg Ile Trp Asp Met Leu Phe Gln Glu Tyr Gln Ser 340 345 350 Arg Leu Asp Asn Arg Arg Ala Glu Gly Ser Glu Asp Arg Ala Glu Ala 355 360 365 Ala Val Leu Glu Glu Val Arg Thr Gln Leu Leu Gly Gly Arg Phe Val 370 375 380 Ser Ala Leu Thr Gly Ser Ala Pro Ile Ser Ala Glu Met Lys Ser Trp385 390 395 400 Val Glu Asp Leu Leu Asp Met His Leu Leu Glu Gly Tyr Gly Ser Thr 405 410 415 Glu Ala Gly Ala Val Phe Ile Asp Gly Gln Ile Gln Arg Pro Pro Val 420 425 430 Ile Asp Tyr Lys Leu Val Asp Val Pro Asp Leu Gly Tyr Phe Ala Thr 435 440 445 Asp Arg Pro Tyr Pro Arg Gly Glu Leu Leu Val Lys Ser Glu Gln Met 450 455 460 Phe Pro Gly Tyr Tyr Lys Arg Pro Glu Ile Thr Ala Glu Met Phe Asp465 470 475 480 Glu Asp Gly Tyr Tyr Arg Thr Gly Asp Ile Val Ala Glu Leu Gly Pro 485 490 495 Asp His Leu Glu Tyr Leu Asp Arg Arg Asn Asn Val Leu Lys Leu Ser 500 505 510 Gln Gly Glu Phe Val Thr Val Ser Lys Leu Glu Ala Val Phe Gly Asp 515 520 525 Ser Pro Leu Val Arg Gln Ile Tyr Val Tyr Gly Asn Ser Ala Arg Ser 530 535 540 Tyr Leu Leu Ala Val Val Val Pro Thr Glu Glu Ala Leu Ser Arg Trp545 550 555 560 Asp Gly Asp Glu Leu Lys Ser Arg Ile Ser Asp Ser Leu Gln Asp Ala 565 570 575 Ala Arg Ala Ala Gly Leu Gln Ser Tyr Glu Ile Pro Arg Asp Phe Leu 580 585 590 Val Glu Thr Thr Pro Phe Thr Leu Glu Asn Gly Leu Leu Thr Gly Ile 595 600 605 Arg Lys Leu Ala Arg Pro Lys Leu Lys Ala His Tyr Gly Glu Arg Leu 610 615 620 Glu Gln Leu Tyr Thr Asp Leu Ala Glu Gly Gln Ala Asn Glu Leu Arg625 630 635 640 Glu Leu Arg Arg Asn Gly Ala Asp Arg Pro Val Val Glu Thr Val Ser 645 650 655 Arg Ala Ala Val Ala Leu Leu Gly Ala Ser Val Thr Asp Leu Arg Ser 660 665 670 Asp Ala His Phe Thr Asp Leu Gly Gly Asp Ser Leu Ser Ala Leu Ser 675 680 685 Phe Ser Asn Leu Leu His Glu Ile Phe Asp Val Asp Val Pro Val Gly 690 695 700 Val Ile Val Ser Pro Ala Thr Asp Leu Ala Gly Val Ala Ala Tyr Ile705 710 715 720 Glu Gly Glu Leu Arg Gly Ser Lys Arg Pro Thr Tyr Ala Ser Val His 725 730 735 Gly Arg Asp Ala Thr Glu Val Arg Ala Arg Asp Leu Ala Leu Gly Lys 740 745 750 Phe Ile Asp Ala Lys Thr Leu Ser Ala Ala Pro Gly Leu Pro Arg Ser 755 760 765 Gly Thr Glu Ile Arg Thr Val Leu Leu Thr Gly Ala Thr Gly Phe Leu 770 775 780 Gly Arg Tyr Leu Ala Leu Glu Trp Leu Glu Arg Met Asp Leu Val Asp785 790 795 800 Gly Lys Val Ile Cys Leu Val Arg Ala Arg Ser Asp Asp Glu Ala Arg 805 810 815 Ala Arg Leu Asp Ala Thr Phe Asp Thr Gly Asp Ala Thr Leu Leu Glu 820 825 830 His Tyr Arg Ala Leu Ala Ala Asp His Leu Glu Val Ile Ala Gly Asp 835 840 845 Lys Gly Glu Ala Asp Leu Gly Leu Asp His Asp Thr Trp Gln Arg Leu 850 855 860 Ala Asp Thr Val Asp Leu Ile Val Asp Pro Ala Ala Leu Val Asn His865 870 875 880 Val Leu Pro Tyr Ser Gln Met Phe Gly Pro Asn Ala Leu Gly Thr Ala 885 890 895 Glu Leu Ile Arg Ile Ala Leu Thr Thr Thr Ile Lys Pro Tyr Val Tyr 900 905 910 Val Ser Thr Ile Gly Val Gly Gln Gly Ile Ser Pro Glu Ala Phe Val 915 920 925 Glu Asp Ala Asp Ile Arg Glu Ile Ser Ala Thr Arg Arg Val Asp Asp 930 935 940 Ser Tyr Ala Asn Gly Tyr Gly Asn Ser Lys Trp Ala Gly Glu Val Leu945 950 955 960 Leu Arg Glu Ala His Asp Trp Cys Gly Leu Pro Val Ser Val Phe Arg 965 970 975 Cys Asp Met Ile Leu Ala Asp Thr Thr Tyr Ser Gly Gln Leu Asn Leu 980 985 990 Pro Asp Met Phe Thr Arg Leu Met Leu Ser Leu Val Ala Thr Gly Ile 995 1000 1005 Ala Pro Gly Ser Phe Tyr Glu Leu Asp Ala Asp Gly Asn Arg Gln Arg 1010 1015 1020 Ala His Tyr Asp Gly Leu Pro Val Glu Phe Ile Ala Glu Ala Ile Ser1025 1030 1035 1040 Thr Ile Gly Ser Gln Val Thr Asp Gly Phe Glu Thr Phe His Val Met 1045 1050 1055 Asn Pro Tyr Asp Asp Gly Ile Gly Leu Asp Glu Tyr Val Asp Trp Leu 1060 1065 1070 Ile Glu Ala Gly Tyr Pro Val His Arg Val Asp Asp Tyr Ala Thr Trp 1075 1080 1085 Leu Ser Arg Phe Glu Thr Ala Leu Arg Ala Leu Pro Glu Arg Gln Arg 1090 1095 1100 Gln Ala Ser Leu Leu Pro Leu Leu His Asn Tyr Gln Gln Pro Ser Pro1105 1110 1115 1120 Pro Val Cys Gly Ala Met Ala Pro Thr Asp Arg Phe Arg Ala Ala Val 1125 1130 1135 Gln Asp Ala Lys Ile Gly Pro Asp Lys Asp Ile Pro His Val Thr Ala 1140 1145 1150 Asp Val Ile Val Lys Tyr Ile Ser Asn Leu Gln Met Leu Gly Leu Leu 1155 1160 1165 111185PRTMycobacterium massiliense 11Met Thr Asn Glu Thr Asn Pro Gln Gln Glu Gln Leu Ser Arg Arg Ile1 5 10 15 Glu Ser Leu Arg Glu Ser Asp Pro Gln Phe Arg Ala Ala Gln Pro Asp 20 25 30 Pro Ala Val Ala Glu Gln Val Leu Arg Pro Gly Leu His Leu Ser Glu 35 40 45 Ala Ile Ala Ala Leu Met Thr Gly Tyr Ala Glu Arg Pro Ala Leu Gly 50 55 60 Glu Arg Ala Arg Glu Leu Val Ile Asp Gln Asp Gly Arg Thr Thr Leu65 70 75 80 Arg Leu Leu Pro Arg Phe Asp Thr Thr Thr Tyr Gly Glu Leu Trp Ser 85 90 95 Arg Thr Thr Ser Val Ala Ala Ala Trp His His Asp Ala Thr His Pro 100 105 110 Val Lys Ala Gly Asp Leu Val Ala Thr Leu Gly Phe Thr Ser Ile Asp 115 120 125 Tyr Thr Val Leu Asp Leu Ala Ile Met Ile Leu Gly Gly Val Ala Val 130 135 140 Pro Leu Gln Thr Ser Ala Pro Ala Ser Gln Trp Thr Thr Ile Leu Ala145 150 155 160 Glu Ala Glu Pro Asn Thr Leu Ala Val Ser Ile Glu Leu Ile Gly Ala 165 170 175 Ala Met Glu Ser Val Arg Ala Thr Pro Ser Ile Lys Gln Val Val Val 180 185 190 Phe Asp Tyr Thr Pro Glu Val Asp Asp Gln Arg Glu Ala Phe Glu Ala 195 200 205 Ala Ser Thr Gln Leu Ala Gly Thr Gly Ile Ala Leu Glu Thr Leu Asp 210 215 220 Ala Val Ile Ala Arg Gly Ala Ala Leu Pro Ala Ala Pro Leu Tyr Ala225 230 235 240 Pro Ser Ala Gly Asp Asp Pro Leu Ala Leu Leu Ile Tyr Thr Ser Gly 245 250 255 Ser Thr Gly Ala Pro Lys Gly Ala Met His Ser Glu Asn Ile Val Arg 260 265 270 Arg Trp Trp Ile Arg Glu Asp Val Met Ala Gly Thr Glu Asn Leu Pro 275 280 285 Met Ile Gly Leu Asn Phe Met Pro Met Ser His Ile Met Gly Arg Gly 290 295 300 Thr Leu Thr Ser Thr Leu Ser Thr Gly Gly Thr Gly Tyr Phe Ala Ala305 310 315 320 Ser Ser Asp Met Ser Thr Leu Phe Glu Asp Met Glu Leu Ile Arg Pro 325 330 335 Thr Ala Leu Ala Leu Val Pro Arg Val Cys Asp Met Val Phe Gln Arg 340

345 350 Phe Gln Thr Glu Val Asp Arg Arg Leu Ala Ser Gly Asp Thr Ala Ser 355 360 365 Ala Glu Ala Val Ala Ala Glu Val Lys Ala Asp Ile Arg Asp Asn Leu 370 375 380 Phe Gly Gly Arg Val Ser Ala Val Met Val Gly Ser Ala Pro Leu Ser385 390 395 400 Glu Glu Leu Gly Glu Phe Ile Glu Ser Cys Phe Glu Leu Asn Leu Thr 405 410 415 Asp Gly Tyr Gly Ser Thr Glu Ala Gly Met Val Phe Arg Asp Gly Ile 420 425 430 Val Gln Arg Pro Pro Val Ile Asp Tyr Lys Leu Val Asp Val Pro Glu 435 440 445 Leu Gly Tyr Phe Ser Thr Asp Lys Pro His Pro Arg Gly Glu Leu Leu 450 455 460 Leu Lys Thr Asp Gly Met Phe Leu Gly Tyr Tyr Lys Arg Pro Glu Val465 470 475 480 Thr Ala Ser Val Phe Asp Ala Asp Gly Phe Tyr Met Thr Gly Asp Ile 485 490 495 Val Ala Glu Leu Ala His Asp Asn Ile Glu Ile Ile Asp Arg Arg Asn 500 505 510 Asn Val Leu Lys Leu Ser Gln Gly Glu Phe Val Ala Val Ala Thr Leu 515 520 525 Glu Ala Glu Tyr Ala Asn Ser Pro Val Val His Gln Ile Tyr Val Tyr 530 535 540 Gly Ser Ser Glu Arg Ser Tyr Leu Leu Ala Val Val Val Pro Thr Pro545 550 555 560 Glu Ala Val Ala Ala Ala Lys Gly Asp Ala Ala Ala Leu Lys Thr Thr 565 570 575 Ile Ala Asp Ser Leu Gln Asp Ile Ala Lys Glu Ile Gln Leu Gln Ser 580 585 590 Tyr Glu Val Pro Arg Asp Phe Ile Ile Glu Pro Gln Pro Phe Thr Gln 595 600 605 Gly Asn Gly Leu Leu Thr Gly Ile Ala Lys Leu Ala Arg Pro Asn Leu 610 615 620 Lys Ala His Tyr Gly Pro Arg Leu Glu Gln Met Tyr Ala Glu Ile Ala625 630 635 640 Glu Gln Gln Ala Ala Glu Leu Arg Ala Leu His Gly Val Asp Pro Asp 645 650 655 Lys Pro Ala Leu Glu Thr Val Leu Lys Ala Ala Gln Ala Leu Leu Gly 660 665 670 Val Ser Ser Ala Glu Leu Ala Ala Asp Ala His Phe Thr Asp Leu Gly 675 680 685 Gly Asp Ser Leu Ser Ala Leu Ser Phe Ser Asp Leu Leu Arg Asp Ile 690 695 700 Phe Ala Val Glu Val Pro Val Gly Val Ile Val Ser Ala Ala Asn Asp705 710 715 720 Leu Gly Gly Val Ala Lys Phe Val Asp Glu Gln Arg His Ser Gly Gly 725 730 735 Thr Arg Pro Thr Ala Glu Thr Val His Gly Ala Gly His Thr Glu Ile 740 745 750 Arg Ala Ala Asp Leu Thr Leu Asp Lys Phe Ile Asp Glu Ala Thr Leu 755 760 765 His Ala Ala Pro Ser Leu Pro Lys Ala Ala Gly Ile Pro His Thr Val 770 775 780 Leu Leu Thr Gly Ser Asn Gly Tyr Leu Gly His Tyr Leu Ala Leu Glu785 790 795 800 Trp Leu Glu Arg Leu Asp Lys Thr Asp Gly Lys Leu Ile Val Ile Val 805 810 815 Arg Gly Lys Asn Ala Glu Ala Ala Tyr Gly Arg Leu Glu Glu Ala Phe 820 825 830 Asp Thr Gly Asp Thr Glu Leu Leu Ala His Phe Arg Ser Leu Ala Asp 835 840 845 Lys His Leu Glu Val Leu Ala Gly Asp Ile Gly Asp Pro Asn Leu Gly 850 855 860 Leu Asp Ala Asp Thr Trp Gln Arg Leu Ala Asp Thr Val Asp Val Ile865 870 875 880 Val His Pro Ala Ala Leu Val Asn His Val Leu Pro Tyr Asn Gln Leu 885 890 895 Phe Gly Pro Asn Val Val Gly Thr Ala Glu Ile Ile Lys Leu Ala Ile 900 905 910 Thr Thr Lys Ile Lys Pro Val Thr Tyr Leu Ser Thr Val Ala Val Ala 915 920 925 Ala Tyr Val Asp Pro Thr Thr Phe Asp Glu Glu Ser Asp Ile Arg Leu 930 935 940 Ile Ser Ala Val Arg Pro Ile Asp Asp Gly Tyr Ala Asn Gly Tyr Gly945 950 955 960 Asn Ala Lys Trp Ala Gly Glu Val Leu Leu Arg Glu Ala His Asp Leu 965 970 975 Cys Gly Leu Pro Val Ala Val Phe Arg Ser Asp Met Ile Leu Ala His 980 985 990 Ser Arg Tyr Thr Gly Gln Leu Asn Val Pro Asp Gln Phe Thr Arg Leu 995 1000 1005 Ile Leu Ser Leu Ile Ala Thr Gly Ile Ala Pro Gly Ser Phe Tyr Gln 1010 1015 1020 Ala Gln Thr Thr Gly Glu Arg Pro Leu Ala His Tyr Asp Gly Leu Pro1025 1030 1035 1040 Gly Asp Phe Thr Ala Glu Ala Ile Thr Thr Leu Gly Thr Gln Val Pro 1045 1050 1055 Glu Gly Ser Glu Gly Phe Val Thr Tyr Asp Cys Val Asn Pro His Ala 1060 1065 1070 Asp Gly Ile Ser Leu Asp Asn Phe Val Asp Trp Leu Ile Glu Ala Gly 1075 1080 1085 Tyr Pro Ile Ala Arg Ile Asp Asn Tyr Thr Glu Trp Phe Thr Arg Phe 1090 1095 1100 Asp Thr Ala Ile Arg Gly Leu Ser Glu Lys Gln Lys Gln His Ser Leu1105 1110 1115 1120 Leu Pro Leu Leu His Ala Phe Glu Gln Pro Ser Ala Ala Glu Asn His 1125 1130 1135 Gly Val Val Pro Ala Lys Arg Phe Gln His Ala Val Gln Ala Ala Gly 1140 1145 1150 Ile Gly Pro Val Gly Gln Asp Gly Thr Thr Asp Ile Pro His Leu Ser 1155 1160 1165 Arg Arg Leu Ile Val Lys Tyr Ala Lys Asp Leu Glu Gln Leu Gly Leu 1170 1175 1180 Leu1185121186PRTSegniliparus rotundus 12Met Thr Gln Ser His Thr Gln Gly Pro Gln Ala Ser Ala Ala His Ser1 5 10 15 Arg Leu Ala Arg Arg Ala Ala Glu Leu Leu Ala Thr Asp Pro Gln Ala 20 25 30 Ala Ala Thr Leu Pro Asp Pro Glu Val Val Arg Gln Ala Thr Arg Pro 35 40 45 Gly Leu Arg Leu Ala Glu Arg Val Asp Ala Ile Leu Ser Gly Tyr Ala 50 55 60 Asp Arg Pro Ala Leu Gly Gln Arg Ser Phe Gln Thr Val Lys Asp Pro65 70 75 80 Ile Thr Gly Arg Ser Ser Val Glu Leu Leu Pro Thr Phe Asp Thr Ile 85 90 95 Thr Tyr Arg Glu Leu Arg Glu Arg Ala Thr Ala Ile Ala Ser Asp Leu 100 105 110 Ala His His Pro Gln Ala Pro Ala Lys Pro Gly Asp Phe Leu Ala Ser 115 120 125 Ile Gly Phe Ile Ser Val Asp Tyr Val Ala Ile Asp Ile Ala Gly Val 130 135 140 Phe Ala Gly Leu Thr Ala Val Pro Leu Gln Thr Gly Ala Thr Leu Ala145 150 155 160 Thr Leu Thr Ala Ile Thr Ala Glu Thr Ala Pro Thr Leu Phe Ala Ala 165 170 175 Ser Ile Glu His Leu Pro Thr Ala Val Asp Ala Val Leu Ala Thr Pro 180 185 190 Ser Val Arg Arg Leu Leu Val Phe Asp Tyr Arg Ala Gly Ser Asp Glu 195 200 205 Asp Arg Glu Ala Val Glu Ala Ala Lys Arg Lys Ile Ala Asp Ala Gly 210 215 220 Ser Ser Val Leu Val Asp Val Leu Asp Glu Val Ile Ala Arg Gly Lys225 230 235 240 Ser Ala Pro Lys Ala Pro Leu Pro Pro Ala Thr Asp Ala Gly Asp Asp 245 250 255 Ser Leu Ser Leu Leu Ile Tyr Thr Ser Gly Ser Thr Gly Thr Pro Lys 260 265 270 Gly Ala Met Tyr Pro Glu Arg Asn Val Ala His Phe Trp Gly Gly Val 275 280 285 Trp Ala Ala Ala Phe Asp Glu Asp Ala Ala Pro Pro Val Pro Ala Ile 290 295 300 Asn Ile Thr Phe Leu Pro Leu Ser His Val Ala Ser Arg Leu Ser Leu305 310 315 320 Met Pro Thr Leu Ala Arg Gly Gly Leu Met His Phe Val Ala Lys Ser 325 330 335 Asp Leu Ser Thr Leu Phe Glu Asp Leu Lys Leu Ala Arg Pro Thr Asn 340 345 350 Leu Phe Leu Val Pro Arg Val Val Glu Met Leu Tyr Gln His Tyr Gln 355 360 365 Ser Glu Leu Asp Arg Arg Gly Val Gln Asp Gly Thr Arg Glu Ala Glu 370 375 380 Ala Val Lys Asp Asp Leu Arg Thr Gly Leu Leu Gly Gly Arg Ile Leu385 390 395 400 Thr Ala Gly Phe Gly Ser Ala Pro Leu Ser Ala Glu Leu Ala Gly Phe 405 410 415 Ile Glu Ser Leu Leu Gln Ile His Leu Val Asp Gly Tyr Gly Ser Thr 420 425 430 Glu Ala Gly Pro Val Trp Arg Asp Gly Tyr Leu Val Lys Pro Pro Val 435 440 445 Thr Asp Tyr Lys Leu Ile Asp Val Pro Glu Leu Gly Tyr Phe Ser Thr 450 455 460 Asp Ser Pro His Pro Arg Gly Glu Leu Ala Ile Lys Thr Gln Thr Ile465 470 475 480 Leu Pro Gly Tyr Tyr Lys Arg Pro Glu Thr Thr Ala Glu Val Phe Asp 485 490 495 Glu Asp Gly Phe Tyr Leu Thr Gly Asp Val Val Ala Gln Ile Gly Pro 500 505 510 Glu Gln Phe Ala Tyr Val Asp Arg Arg Lys Asn Val Leu Lys Leu Ser 515 520 525 Gln Gly Glu Phe Val Thr Leu Ala Lys Leu Glu Ala Ala Tyr Ser Ser 530 535 540 Ser Pro Leu Val Arg Gln Leu Phe Val Tyr Gly Ser Ser Glu Arg Ser545 550 555 560 Tyr Leu Leu Ala Val Ile Val Pro Thr Pro Asp Ala Leu Lys Lys Phe 565 570 575 Gly Val Gly Glu Ala Ala Lys Ala Ala Leu Gly Glu Ser Leu Gln Lys 580 585 590 Ile Ala Arg Asp Glu Gly Leu Gln Ser Tyr Glu Val Pro Arg Asp Phe 595 600 605 Ile Ile Glu Thr Asp Pro Phe Thr Val Glu Asn Gly Leu Leu Ser Asp 610 615 620 Ala Arg Lys Ser Leu Arg Pro Lys Leu Lys Glu His Tyr Gly Glu Arg625 630 635 640 Leu Glu Ala Met Tyr Lys Glu Leu Ala Asp Gly Gln Ala Asn Glu Leu 645 650 655 Arg Asp Ile Arg Arg Gly Val Gln Gln Arg Pro Thr Leu Glu Thr Val 660 665 670 Arg Arg Ala Ala Ala Ala Met Leu Gly Ala Ser Ala Ala Glu Ile Lys 675 680 685 Pro Asp Ala His Phe Thr Asp Leu Gly Gly Asp Ser Leu Ser Ala Leu 690 695 700 Thr Phe Ser Asn Phe Leu His Asp Leu Phe Glu Val Asp Val Pro Val705 710 715 720 Gly Val Ile Val Ser Ala Ala Asn Thr Leu Gly Ser Val Ala Glu His 725 730 735 Ile Asp Ala Gln Leu Ala Gly Gly Arg Ala Arg Pro Thr Phe Ala Thr 740 745 750 Val His Gly Lys Gly Ser Thr Thr Ile Lys Ala Ser Asp Leu Thr Leu 755 760 765 Asp Lys Phe Ile Asp Glu Gln Thr Leu Glu Ala Ala Lys His Leu Pro 770 775 780 Lys Pro Ala Asp Pro Pro Arg Thr Val Leu Leu Thr Gly Ala Asn Gly785 790 795 800 Trp Leu Gly Arg Phe Leu Ala Leu Glu Trp Leu Glu Arg Leu Ala Pro 805 810 815 Ala Gly Gly Lys Leu Ile Thr Ile Val Arg Gly Lys Asp Ala Ala Gln 820 825 830 Ala Lys Ala Arg Leu Asp Ala Ala Tyr Glu Ser Gly Asp Pro Lys Leu 835 840 845 Ala Gly His Tyr Gln Asp Leu Ala Ala Thr Thr Leu Glu Val Leu Ala 850 855 860 Gly Asp Phe Ser Glu Pro Arg Leu Gly Leu Asp Glu Ala Thr Trp Asn865 870 875 880 Arg Leu Ala Asp Glu Val Asp Phe Ile Ser His Pro Gly Ala Leu Val 885 890 895 Asn His Val Leu Pro Tyr Asn Gln Leu Phe Gly Pro Asn Val Ala Gly 900 905 910 Val Ala Glu Ile Ile Lys Leu Ala Ile Thr Thr Arg Ile Lys Pro Val 915 920 925 Thr Tyr Leu Ser Thr Val Ala Val Ala Ala Gly Val Glu Pro Ser Ala 930 935 940 Leu Asp Glu Asp Gly Asp Ile Arg Thr Val Ser Ala Glu Arg Ser Val945 950 955 960 Asp Glu Gly Tyr Ala Asn Gly Tyr Gly Asn Ser Lys Trp Gly Gly Glu 965 970 975 Val Leu Leu Arg Glu Ala His Asp Arg Thr Gly Leu Pro Val Arg Val 980 985 990 Phe Arg Ser Asp Met Ile Leu Ala His Gln Lys Tyr Thr Gly Gln Val 995 1000 1005 Asn Ala Thr Asp Gln Phe Thr Arg Leu Val Gln Ser Leu Leu Ala Thr 1010 1015 1020 Gly Leu Ala Pro Lys Ser Phe Tyr Glu Leu Asp Ala Gln Gly Asn Arg1025 1030 1035 1040 Gln Arg Ala His Tyr Asp Gly Ile Pro Val Asp Phe Thr Ala Glu Ser 1045 1050 1055 Ile Thr Thr Leu Gly Gly Asp Gly Leu Glu Gly Tyr Arg Ser Tyr Asn 1060 1065 1070 Val Phe Asn Pro His Arg Asp Gly Val Gly Leu Asp Glu Phe Val Asp 1075 1080 1085 Trp Leu Ile Glu Ala Gly His Pro Ile Thr Arg Ile Asp Asp Tyr Asp 1090 1095 1100 Gln Trp Leu Ser Arg Phe Glu Thr Ser Leu Arg Gly Leu Pro Glu Ser1105 1110 1115 1120 Lys Arg Gln Ala Ser Val Leu Pro Leu Leu His Ala Phe Ala Arg Pro 1125 1130 1135 Gly Pro Ala Val Asp Gly Ser Pro Phe Arg Asn Thr Val Phe Arg Thr 1140 1145 1150 Asp Val Gln Lys Ala Lys Ile Gly Ala Glu His Asp Ile Pro His Leu 1155 1160 1165 Gly Lys Ala Leu Val Leu Lys Tyr Ala Asp Asp Ile Lys Gln Leu Gly 1170 1175 1180 Leu Leu1185 13459PRTChromobacterium violaceum 13Met Gln Lys Gln Arg Thr Thr Ser Gln Trp Arg Glu Leu Asp Ala Ala1 5 10 15 His His Leu His Pro Phe Thr Asp Thr Ala Ser Leu Asn Gln Ala Gly 20 25 30 Ala Arg Val Met Thr Arg Gly Glu Gly Val Tyr Leu Trp Asp Ser Glu 35 40 45 Gly Asn Lys Ile Ile Asp Gly Met Ala Gly Leu Trp Cys Val Asn Val 50 55 60 Gly Tyr Gly Arg Lys Asp Phe Ala Glu Ala Ala Arg Arg Gln Met Glu65 70 75 80 Glu Leu Pro Phe Tyr Asn Thr Phe Phe Lys Thr Thr His Pro Ala Val 85 90 95 Val Glu Leu Ser Ser Leu Leu Ala Glu Val Thr Pro Ala Gly Phe Asp 100 105 110 Arg Val Phe Tyr Thr Asn Ser Gly Ser Glu Ser Val Asp Thr Met Ile 115 120 125 Arg Met Val Arg Arg Tyr Trp Asp Val Gln Gly Lys Pro Glu Lys Lys 130 135 140 Thr Leu Ile Gly Arg Trp Asn Gly Tyr His Gly Ser Thr Ile Gly Gly145 150 155 160 Ala Ser Leu Gly Gly Met Lys Tyr Met His Glu Gln Gly Asp Leu Pro 165 170 175 Ile Pro Gly Met Ala His Ile Glu Gln Pro Trp Trp Tyr Lys His Gly 180 185 190 Lys Asp Met Thr Pro Asp Glu Phe Gly Val Val Ala Ala Arg Trp Leu 195 200 205 Glu Glu Lys Ile Leu Glu Ile Gly Ala Asp Lys Val Ala Ala Phe Val 210 215 220 Gly Glu Pro Ile Gln Gly Ala Gly Gly Val Ile Val Pro Pro Ala Thr225 230 235 240 Tyr Trp Pro Glu Ile Glu Arg Ile Cys Arg Lys Tyr Asp Val Leu Leu 245 250 255 Val Ala Asp Glu Val Ile Cys Gly Phe Gly Arg Thr Gly Glu Trp Phe 260 265 270 Gly His Gln His Phe Gly Phe Gln Pro Asp Leu Phe Thr Ala Ala

Lys 275 280 285 Gly Leu Ser Ser Gly Tyr Leu Pro Ile Gly Ala Val Phe Val Gly Lys 290 295 300 Arg Val Ala Glu Gly Leu Ile Ala Gly Gly Asp Phe Asn His Gly Phe305 310 315 320 Thr Tyr Ser Gly His Pro Val Cys Ala Ala Val Ala His Ala Asn Val 325 330 335 Ala Ala Leu Arg Asp Glu Gly Ile Val Gln Arg Val Lys Asp Asp Ile 340 345 350 Gly Pro Tyr Met Gln Lys Arg Trp Arg Glu Thr Phe Ser Arg Phe Glu 355 360 365 His Val Asp Asp Val Arg Gly Val Gly Met Val Gln Ala Phe Thr Leu 370 375 380 Val Lys Asn Lys Ala Lys Arg Glu Leu Phe Pro Asp Phe Gly Glu Ile385 390 395 400 Gly Thr Leu Cys Arg Asp Ile Phe Phe Arg Asn Asn Leu Ile Met Arg 405 410 415 Ala Cys Gly Asp His Ile Val Ser Ala Pro Pro Leu Val Met Thr Arg 420 425 430 Ala Glu Val Asp Glu Met Leu Ala Val Ala Glu Arg Cys Leu Glu Glu 435 440 445 Phe Glu Gln Thr Leu Lys Ala Arg Gly Leu Ala 450 455 14468PRTPseudomonas aeruginosa 14Met Asn Ala Arg Leu His Ala Thr Ser Pro Leu Gly Asp Ala Asp Leu1 5 10 15 Val Arg Ala Asp Gln Ala His Tyr Met His Gly Tyr His Val Phe Asp 20 25 30 Asp His Arg Val Asn Gly Ser Leu Asn Ile Ala Ala Gly Asp Gly Ala 35 40 45 Tyr Ile Tyr Asp Thr Ala Gly Asn Arg Tyr Leu Asp Ala Val Gly Gly 50 55 60 Met Trp Cys Thr Asn Ile Gly Leu Gly Arg Glu Glu Met Ala Arg Thr65 70 75 80 Val Ala Glu Gln Thr Arg Leu Leu Ala Tyr Ser Asn Pro Phe Cys Asp 85 90 95 Met Ala Asn Pro Arg Ala Ile Glu Leu Cys Arg Lys Leu Ala Glu Leu 100 105 110 Ala Pro Gly Asp Leu Asp His Val Phe Leu Thr Thr Gly Gly Ser Thr 115 120 125 Ala Val Asp Thr Ala Ile Arg Leu Met His Tyr Tyr Gln Asn Cys Arg 130 135 140 Gly Lys Arg Ala Lys Lys His Val Ile Thr Arg Ile Asn Ala Tyr His145 150 155 160 Gly Ser Thr Phe Leu Gly Met Ser Leu Gly Gly Lys Ser Ala Asp Arg 165 170 175 Pro Ala Glu Phe Asp Phe Leu Asp Glu Arg Ile His His Leu Ala Cys 180 185 190 Pro Tyr Tyr Tyr Arg Ala Pro Glu Gly Leu Gly Glu Ala Glu Phe Leu 195 200 205 Asp Gly Leu Val Asp Glu Phe Glu Arg Lys Ile Leu Glu Leu Gly Ala 210 215 220 Asp Arg Val Gly Ala Phe Ile Ser Glu Pro Val Phe Gly Ser Gly Gly225 230 235 240 Val Ile Val Pro Pro Ala Gly Tyr His Arg Arg Met Trp Glu Leu Cys 245 250 255 Gln Arg Tyr Asp Val Leu Tyr Ile Ser Asp Glu Val Val Thr Ser Phe 260 265 270 Gly Arg Leu Gly His Phe Phe Ala Ser Gln Ala Val Phe Gly Val Gln 275 280 285 Pro Asp Ile Ile Leu Thr Ala Lys Gly Leu Thr Ser Gly Tyr Gln Pro 290 295 300 Leu Gly Ala Cys Ile Phe Ser Arg Arg Ile Trp Glu Val Ile Ala Glu305 310 315 320 Pro Asp Lys Gly Arg Cys Phe Ser His Gly Phe Thr Tyr Ser Gly His 325 330 335 Pro Val Ala Cys Ala Ala Ala Leu Lys Asn Ile Glu Ile Ile Glu Arg 340 345 350 Glu Gly Leu Leu Ala His Ala Asp Glu Val Gly Arg Tyr Phe Glu Glu 355 360 365 Arg Leu Gln Ser Leu Arg Asp Leu Pro Ile Val Gly Asp Val Arg Gly 370 375 380 Met Arg Phe Met Ala Cys Val Glu Phe Val Ala Asp Lys Ala Ser Lys385 390 395 400 Ala Leu Phe Pro Glu Ser Leu Asn Ile Gly Glu Trp Val His Leu Arg 405 410 415 Ala Gln Lys Arg Gly Leu Leu Val Arg Pro Ile Val His Leu Asn Val 420 425 430 Met Ser Pro Pro Leu Ile Leu Thr Arg Glu Gln Val Asp Thr Val Val 435 440 445 Arg Val Leu Arg Glu Ser Ile Glu Glu Thr Val Glu Asp Leu Val Arg 450 455 460 Ala Gly His Arg465 15454PRTPseudomonas syringae 15Met Ser Ala Asn Asn Pro Gln Thr Leu Glu Trp Gln Ala Leu Ser Ser1 5 10 15 Glu His His Leu Ala Pro Phe Ser Asp Tyr Lys Gln Leu Lys Glu Lys 20 25 30 Gly Pro Arg Ile Ile Thr Arg Ala Glu Gly Val Tyr Leu Trp Asp Ser 35 40 45 Glu Gly Asn Lys Ile Leu Asp Gly Met Ser Gly Leu Trp Cys Val Ala 50 55 60 Ile Gly Tyr Gly Arg Glu Glu Leu Ala Asp Ala Ala Ser Lys Gln Met65 70 75 80 Arg Glu Leu Pro Tyr Tyr Asn Leu Phe Phe Gln Thr Ala His Pro Pro 85 90 95 Val Leu Glu Leu Ala Lys Ala Ile Ser Asp Ile Ala Pro Glu Gly Met 100 105 110 Asn His Val Phe Phe Thr Gly Ser Gly Ser Glu Gly Asn Asp Thr Met 115 120 125 Leu Arg Met Val Arg His Tyr Trp Ala Leu Lys Gly Gln Pro Asn Lys 130 135 140 Lys Thr Ile Ile Ser Arg Val Asn Gly Tyr His Gly Ser Thr Val Ala145 150 155 160 Gly Ala Ser Leu Gly Gly Met Thr Tyr Met His Glu Gln Gly Asp Leu 165 170 175 Pro Ile Pro Gly Val Val His Ile Pro Gln Pro Tyr Trp Phe Gly Glu 180 185 190 Gly Gly Asp Met Thr Pro Asp Glu Phe Gly Ile Trp Ala Ala Glu Gln 195 200 205 Leu Glu Lys Lys Ile Leu Glu Leu Gly Val Glu Asn Val Gly Ala Phe 210 215 220 Ile Ala Glu Pro Ile Gln Gly Ala Gly Gly Val Ile Val Pro Pro Asp225 230 235 240 Ser Tyr Trp Pro Lys Ile Lys Glu Ile Leu Ser Arg Tyr Asp Ile Leu 245 250 255 Phe Ala Ala Asp Glu Val Ile Cys Gly Phe Gly Arg Thr Ser Glu Trp 260 265 270 Phe Gly Ser Asp Phe Tyr Gly Leu Arg Pro Asp Met Met Thr Ile Ala 275 280 285 Lys Gly Leu Thr Ser Gly Tyr Val Pro Met Gly Gly Leu Ile Val Arg 290 295 300 Asp Glu Ile Val Ala Val Leu Asn Glu Gly Gly Asp Phe Asn His Gly305 310 315 320 Phe Thr Tyr Ser Gly His Pro Val Ala Ala Ala Val Ala Leu Glu Asn 325 330 335 Ile Arg Ile Leu Arg Glu Glu Lys Ile Val Glu Arg Val Arg Ser Glu 340 345 350 Thr Ala Pro Tyr Leu Gln Lys Arg Leu Arg Glu Leu Ser Asp His Pro 355 360 365 Leu Val Gly Glu Val Arg Gly Val Gly Leu Leu Gly Ala Ile Glu Leu 370 375 380 Val Lys Asp Lys Thr Thr Arg Glu Arg Tyr Thr Asp Lys Gly Ala Gly385 390 395 400 Met Ile Cys Arg Thr Phe Cys Phe Asp Asn Gly Leu Ile Met Arg Ala 405 410 415 Val Gly Asp Thr Met Ile Ile Ala Pro Pro Leu Val Ile Ser Phe Ala 420 425 430 Gln Ile Asp Glu Leu Val Glu Lys Ala Arg Thr Cys Leu Asp Leu Thr 435 440 445 Leu Ala Val Leu Gln Gly 450 16467PRTRhodobacter sphaeroides 16Met Thr Arg Asn Asp Ala Thr Asn Ala Ala Gly Ala Val Gly Ala Ala1 5 10 15 Met Arg Asp His Ile Leu Leu Pro Ala Gln Glu Met Ala Lys Leu Gly 20 25 30 Lys Ser Ala Gln Pro Val Leu Thr His Ala Glu Gly Ile Tyr Val His 35 40 45 Thr Glu Asp Gly Arg Arg Leu Ile Asp Gly Pro Ala Gly Met Trp Cys 50 55 60 Ala Gln Val Gly Tyr Gly Arg Arg Glu Ile Val Asp Ala Met Ala His65 70 75 80 Gln Ala Met Val Leu Pro Tyr Ala Ser Pro Trp Tyr Met Ala Thr Ser 85 90 95 Pro Ala Ala Arg Leu Ala Glu Lys Ile Ala Thr Leu Thr Pro Gly Asp 100 105 110 Leu Asn Arg Ile Phe Phe Thr Thr Gly Gly Ser Thr Ala Val Asp Ser 115 120 125 Ala Leu Arg Phe Ser Glu Phe Tyr Asn Asn Val Leu Gly Arg Pro Gln 130 135 140 Lys Lys Arg Ile Ile Val Arg Tyr Asp Gly Tyr His Gly Ser Thr Ala145 150 155 160 Leu Thr Ala Ala Cys Thr Gly Arg Thr Gly Asn Trp Pro Asn Phe Asp 165 170 175 Ile Ala Gln Asp Arg Ile Ser Phe Leu Ser Ser Pro Asn Pro Arg His 180 185 190 Ala Gly Asn Arg Ser Gln Glu Ala Phe Leu Asp Asp Leu Val Gln Glu 195 200 205 Phe Glu Asp Arg Ile Glu Ser Leu Gly Pro Asp Thr Ile Ala Ala Phe 210 215 220 Leu Ala Glu Pro Ile Leu Ala Ser Gly Gly Val Ile Ile Pro Pro Ala225 230 235 240 Gly Tyr His Ala Arg Phe Lys Ala Ile Cys Glu Lys His Asp Ile Leu 245 250 255 Tyr Ile Ser Asp Glu Val Val Thr Gly Phe Gly Arg Cys Gly Glu Trp 260 265 270 Phe Ala Ser Glu Lys Val Phe Gly Val Val Pro Asp Ile Ile Thr Phe 275 280 285 Ala Lys Gly Val Thr Ser Gly Tyr Val Pro Leu Gly Gly Leu Ala Ile 290 295 300 Ser Glu Ala Val Leu Ala Arg Ile Ser Gly Glu Asn Ala Lys Gly Ser305 310 315 320 Trp Phe Thr Asn Gly Tyr Thr Tyr Ser Asn Gln Pro Val Ala Cys Ala 325 330 335 Ala Ala Leu Ala Asn Ile Glu Leu Met Glu Arg Glu Gly Ile Val Asp 340 345 350 Gln Ala Arg Glu Met Ala Asp Tyr Phe Ala Ala Ala Leu Ala Ser Leu 355 360 365 Arg Asp Leu Pro Gly Val Ala Glu Thr Arg Ser Val Gly Leu Val Gly 370 375 380 Cys Val Gln Cys Leu Leu Asp Pro Thr Arg Ala Asp Gly Thr Ala Glu385 390 395 400 Asp Lys Ala Phe Thr Leu Lys Ile Asp Glu Arg Cys Phe Glu Leu Gly 405 410 415 Leu Ile Val Arg Pro Leu Gly Asp Leu Cys Val Ile Ser Pro Pro Leu 420 425 430 Ile Ile Ser Arg Ala Gln Ile Asp Glu Met Val Ala Ile Met Arg Gln 435 440 445 Ala Ile Thr Glu Val Ser Ala Ala His Gly Leu Thr Ala Lys Glu Pro 450 455 460 Ala Ala Val465 17459PRTEscherichia coli 17Met Asn Arg Leu Pro Ser Ser Ala Ser Ala Leu Ala Cys Ser Ala His1 5 10 15 Ala Leu Asn Leu Ile Glu Lys Arg Thr Leu Asp His Glu Glu Met Lys 20 25 30 Ala Leu Asn Arg Glu Val Ile Glu Tyr Phe Lys Glu His Val Asn Pro 35 40 45 Gly Phe Leu Glu Tyr Arg Lys Ser Val Thr Ala Gly Gly Asp Tyr Gly 50 55 60 Ala Val Glu Trp Gln Ala Gly Ser Leu Asn Thr Leu Val Asp Thr Gln65 70 75 80 Gly Gln Glu Phe Ile Asp Cys Leu Gly Gly Phe Gly Ile Phe Asn Val 85 90 95 Gly His Arg Asn Pro Val Val Val Ser Ala Val Gln Asn Gln Leu Ala 100 105 110 Lys Gln Pro Leu His Ser Gln Glu Leu Leu Asp Pro Leu Arg Ala Met 115 120 125 Leu Ala Lys Thr Leu Ala Ala Leu Thr Pro Gly Lys Leu Lys Tyr Ser 130 135 140 Phe Phe Cys Asn Ser Gly Thr Glu Ser Val Glu Ala Ala Leu Lys Leu145 150 155 160 Ala Lys Ala Tyr Gln Ser Pro Arg Gly Lys Phe Thr Phe Ile Ala Thr 165 170 175 Ser Gly Ala Phe His Gly Lys Ser Leu Gly Ala Leu Ser Ala Thr Ala 180 185 190 Lys Ser Thr Phe Arg Lys Pro Phe Met Pro Leu Leu Pro Gly Phe Arg 195 200 205 His Val Pro Phe Gly Asn Ile Glu Ala Met Arg Thr Ala Leu Asn Glu 210 215 220 Cys Lys Lys Thr Gly Asp Asp Val Ala Ala Val Ile Leu Glu Pro Ile225 230 235 240 Gln Gly Glu Gly Gly Val Ile Leu Pro Pro Pro Gly Tyr Leu Thr Ala 245 250 255 Val Arg Lys Leu Cys Asp Glu Phe Gly Ala Leu Met Ile Leu Asp Glu 260 265 270 Val Gln Thr Gly Met Gly Arg Thr Gly Lys Met Phe Ala Cys Glu His 275 280 285 Glu Asn Val Gln Pro Asp Ile Leu Cys Leu Ala Lys Ala Leu Gly Gly 290 295 300 Gly Val Met Pro Ile Gly Ala Thr Ile Ala Thr Glu Glu Val Phe Ser305 310 315 320 Val Leu Phe Asp Asn Pro Phe Leu His Thr Thr Thr Phe Gly Gly Asn 325 330 335 Pro Leu Ala Cys Ala Ala Ala Leu Ala Thr Ile Asn Val Leu Leu Glu 340 345 350 Gln Asn Leu Pro Ala Gln Ala Glu Gln Lys Gly Asp Met Leu Leu Asp 355 360 365 Gly Phe Arg Gln Leu Ala Arg Glu Tyr Pro Asp Leu Val Gln Glu Ala 370 375 380 Arg Gly Lys Gly Met Leu Met Ala Ile Glu Phe Val Asp Asn Glu Ile385 390 395 400 Gly Tyr Asn Phe Ala Ser Glu Met Phe Arg Gln Arg Val Leu Val Ala 405 410 415 Gly Thr Leu Asn Asn Ala Lys Thr Ile Arg Ile Glu Pro Pro Leu Thr 420 425 430 Leu Thr Ile Glu Gln Cys Glu Leu Val Ile Lys Ala Ala Arg Lys Ala 435 440 445 Leu Ala Ala Met Arg Val Ser Val Glu Glu Ala 450 455 18453PRTVibrio Fluvialis 18Met Asn Lys Pro Gln Ser Trp Glu Ala Arg Ala Glu Thr Tyr Ser Leu1 5 10 15 Tyr Gly Phe Thr Asp Met Pro Ser Leu His Gln Arg Gly Thr Val Val 20 25 30 Val Thr His Gly Glu Gly Pro Tyr Ile Val Asp Val Asn Gly Arg Arg 35 40 45 Tyr Leu Asp Ala Asn Ser Gly Leu Trp Asn Met Val Ala Gly Phe Asp 50 55 60 His Lys Gly Leu Ile Asp Ala Ala Lys Ala Gln Tyr Glu Arg Phe Pro65 70 75 80 Gly Tyr His Ala Phe Phe Gly Arg Met Ser Asp Gln Thr Val Met Leu 85 90 95 Ser Glu Lys Leu Val Glu Val Ser Pro Phe Asp Ser Gly Arg Val Phe 100 105 110 Tyr Thr Asn Ser Gly Ser Glu Ala Asn Asp Thr Met Val Lys Met Leu 115 120 125 Trp Phe Leu His Ala Ala Glu Gly Lys Pro Gln Lys Arg Lys Ile Leu 130 135 140 Thr Arg Trp Asn Ala Tyr His Gly Val Thr Ala Val Ser Ala Ser Met145 150 155 160 Thr Gly Lys Pro Tyr Asn Ser Val Phe Gly Leu Pro Leu Pro Gly Phe 165 170 175 Val His Leu Thr Cys Pro His Tyr Trp Arg Tyr Gly Glu Glu Gly Glu 180 185 190 Thr Glu Glu Gln Phe Val Ala Arg Leu Ala Arg Glu Leu Glu Glu Thr 195 200 205 Ile Gln Arg Glu Gly Ala Asp Thr Ile Ala Gly Phe Phe Ala Glu Pro 210 215 220 Val Met Gly Ala Gly Gly Val Ile Pro Pro Ala Lys Gly Tyr Phe Gln225 230 235 240 Ala Ile Leu Pro Ile Leu Arg Lys Tyr Asp Ile Pro Val Ile Ser Asp 245 250 255 Glu Val Ile Cys Gly Phe Gly Arg Thr Gly

Asn Thr Trp Gly Cys Val 260 265 270 Thr Tyr Asp Phe Thr Pro Asp Ala Ile Ile Ser Ser Lys Asn Leu Thr 275 280 285 Ala Gly Phe Phe Pro Met Gly Ala Val Ile Leu Gly Pro Glu Leu Ser 290 295 300 Lys Arg Leu Glu Thr Ala Ile Glu Ala Ile Glu Glu Phe Pro His Gly305 310 315 320 Phe Thr Ala Ser Gly His Pro Val Gly Cys Ala Ile Ala Leu Lys Ala 325 330 335 Ile Asp Val Val Met Asn Glu Gly Leu Ala Glu Asn Val Arg Arg Leu 340 345 350 Ala Pro Arg Phe Glu Glu Arg Leu Lys His Ile Ala Glu Arg Pro Asn 355 360 365 Ile Gly Glu Tyr Arg Gly Ile Gly Phe Met Trp Ala Leu Glu Ala Val 370 375 380 Lys Asp Lys Ala Ser Lys Thr Pro Phe Asp Gly Asn Leu Ser Val Ser385 390 395 400 Glu Arg Ile Ala Asn Thr Cys Thr Asp Leu Gly Leu Ile Cys Arg Pro 405 410 415 Leu Gly Gln Ser Val Val Leu Cys Pro Pro Phe Ile Leu Thr Glu Ala 420 425 430 Gln Met Asp Glu Met Phe Asp Lys Leu Glu Lys Ala Leu Asp Lys Val 435 440 445 Phe Ala Glu Val Ala 450 19224PRTBacillus subtilis 19Met Lys Ile Tyr Gly Ile Tyr Met Asp Arg Pro Leu Ser Gln Glu Glu1 5 10 15 Asn Glu Arg Phe Met Ser Phe Ile Ser Pro Glu Lys Arg Glu Lys Cys 20 25 30 Arg Arg Phe Tyr His Lys Glu Asp Ala His Arg Thr Leu Leu Gly Asp 35 40 45 Val Leu Val Arg Ser Val Ile Ser Arg Gln Tyr Gln Leu Asp Lys Ser 50 55 60 Asp Ile Arg Phe Ser Thr Gln Glu Tyr Gly Lys Pro Cys Ile Pro Asp65 70 75 80 Leu Pro Asp Ala His Phe Asn Ile Ser His Ser Gly Arg Trp Val Ile 85 90 95 Cys Ala Phe Asp Ser Gln Pro Ile Gly Ile Asp Ile Glu Lys Thr Lys 100 105 110 Pro Ile Ser Leu Glu Ile Ala Lys Arg Phe Phe Ser Lys Thr Glu Tyr 115 120 125 Ser Asp Leu Leu Ala Lys Asp Lys Asp Glu Gln Thr Asp Tyr Phe Tyr 130 135 140 His Leu Trp Ser Met Lys Glu Ser Phe Ile Lys Gln Glu Gly Lys Gly145 150 155 160 Leu Ser Leu Pro Leu Asp Ser Phe Ser Val Arg Leu His Gln Asp Gly 165 170 175 Gln Val Ser Ile Glu Leu Pro Asp Ser His Ser Pro Cys Tyr Ile Lys 180 185 190 Thr Tyr Glu Val Asp Pro Gly Tyr Lys Met Ala Val Cys Ala Ala His 195 200 205 Pro Asp Phe Pro Glu Asp Ile Thr Met Val Ser Tyr Glu Glu Leu Leu 210 215 220 20222PRTNocardia sp. NRRL 5646 20Met Ile Glu Thr Ile Leu Pro Ala Gly Val Glu Ser Ala Glu Leu Leu1 5 10 15 Glu Tyr Pro Glu Asp Leu Lys Ala His Pro Ala Glu Glu His Leu Ile 20 25 30 Ala Lys Ser Val Glu Lys Arg Arg Arg Asp Phe Ile Gly Ala Arg His 35 40 45 Cys Ala Arg Leu Ala Leu Ala Glu Leu Gly Glu Pro Pro Val Ala Ile 50 55 60 Gly Lys Gly Glu Arg Gly Ala Pro Ile Trp Pro Arg Gly Val Val Gly65 70 75 80 Ser Leu Thr His Cys Asp Gly Tyr Arg Ala Ala Ala Val Ala His Lys 85 90 95 Met Arg Phe Arg Ser Ile Gly Ile Asp Ala Glu Pro His Ala Thr Leu 100 105 110 Pro Glu Gly Val Leu Asp Ser Val Ser Leu Pro Pro Glu Arg Glu Trp 115 120 125 Leu Lys Thr Thr Asp Ser Ala Leu His Leu Asp Arg Leu Leu Phe Cys 130 135 140 Ala Lys Glu Ala Thr Tyr Lys Ala Trp Trp Pro Leu Thr Ala Arg Trp145 150 155 160 Leu Gly Phe Glu Glu Ala His Ile Thr Phe Glu Ile Glu Asp Gly Ser 165 170 175 Ala Asp Ser Gly Asn Gly Thr Phe His Ser Glu Leu Leu Val Pro Gly 180 185 190 Gln Thr Asn Asp Gly Gly Thr Pro Leu Leu Ser Phe Asp Gly Arg Trp 195 200 205 Leu Ile Ala Asp Gly Phe Ile Leu Thr Ala Ile Ala Tyr Ala 210 215 220 21286PRTEscherichia coli 21Met Ser Gln Ala Leu Lys Asn Leu Leu Thr Leu Leu Asn Leu Glu Lys1 5 10 15 Ile Glu Glu Gly Leu Phe Arg Gly Gln Ser Glu Asp Leu Gly Leu Arg 20 25 30 Gln Val Phe Gly Gly Gln Val Val Gly Gln Ala Leu Tyr Ala Ala Lys 35 40 45 Glu Thr Val Pro Glu Glu Arg Leu Val His Ser Phe His Ser Tyr Phe 50 55 60 Leu Arg Pro Gly Asp Ser Lys Lys Pro Ile Ile Tyr Asp Val Glu Thr65 70 75 80 Leu Arg Asp Gly Asn Ser Phe Ser Ala Arg Arg Val Ala Ala Ile Gln 85 90 95 Asn Gly Lys Pro Ile Phe Tyr Met Thr Ala Ser Phe Gln Ala Pro Glu 100 105 110 Ala Gly Phe Glu His Gln Lys Thr Met Pro Ser Ala Pro Ala Pro Asp 115 120 125 Gly Leu Pro Ser Glu Thr Gln Ile Ala Gln Ser Leu Ala His Leu Leu 130 135 140 Pro Pro Val Leu Lys Asp Lys Phe Ile Cys Asp Arg Pro Leu Glu Val145 150 155 160 Arg Pro Val Glu Phe His Asn Pro Leu Lys Gly His Val Ala Glu Pro 165 170 175 His Arg Gln Val Trp Ile Arg Ala Asn Gly Ser Val Pro Asp Asp Leu 180 185 190 Arg Val His Gln Tyr Leu Leu Gly Tyr Ala Ser Asp Leu Asn Phe Leu 195 200 205 Pro Val Ala Leu Gln Pro His Gly Ile Gly Phe Leu Glu Pro Gly Ile 210 215 220 Gln Ile Ala Thr Ile Asp His Ser Met Trp Phe His Arg Pro Phe Asn225 230 235 240 Leu Asn Glu Trp Leu Leu Tyr Ser Val Glu Ser Thr Ser Ala Ser Ser 245 250 255 Ala Arg Gly Phe Val Arg Gly Glu Phe Tyr Thr Gln Asp Gly Val Leu 260 265 270 Val Ala Ser Thr Val Gln Glu Gly Val Met Arg Asn His Asn 275 280 285 22561PRTEscherichia coli 22Met Lys Lys Val Trp Leu Asn Arg Tyr Pro Ala Asp Val Pro Thr Glu1 5 10 15 Ile Asn Pro Asp Arg Tyr Gln Ser Leu Val Asp Met Phe Glu Gln Ser 20 25 30 Val Ala Arg Tyr Ala Asp Gln Pro Ala Phe Val Asn Met Gly Glu Val 35 40 45 Met Thr Phe Arg Lys Leu Glu Glu Arg Ser Arg Ala Phe Ala Ala Tyr 50 55 60 Leu Gln Gln Gly Leu Gly Leu Lys Lys Gly Asp Arg Val Ala Leu Met65 70 75 80 Met Pro Asn Leu Leu Gln Tyr Pro Val Ala Leu Phe Gly Ile Leu Arg 85 90 95 Ala Gly Met Ile Val Val Asn Val Asn Pro Leu Tyr Thr Pro Arg Glu 100 105 110 Leu Glu His Gln Leu Asn Asp Ser Gly Ala Ser Ala Ile Val Ile Val 115 120 125 Ser Asn Phe Ala His Thr Leu Glu Lys Val Val Asp Lys Thr Ala Val 130 135 140 Gln His Val Ile Leu Thr Arg Met Gly Asp Gln Leu Ser Thr Ala Lys145 150 155 160 Gly Thr Val Val Asn Phe Val Val Lys Tyr Ile Lys Arg Leu Val Pro 165 170 175 Lys Tyr His Leu Pro Asp Ala Ile Ser Phe Arg Ser Ala Leu His Asn 180 185 190 Gly Tyr Arg Met Gln Tyr Val Lys Pro Glu Leu Val Pro Glu Asp Leu 195 200 205 Ala Phe Leu Gln Tyr Thr Gly Gly Thr Thr Gly Val Ala Lys Gly Ala 210 215 220 Met Leu Thr His Arg Asn Met Leu Ala Asn Leu Glu Gln Val Asn Ala225 230 235 240 Thr Tyr Gly Pro Leu Leu His Pro Gly Lys Glu Leu Val Val Thr Ala 245 250 255 Leu Pro Leu Tyr His Ile Phe Ala Leu Thr Ile Asn Cys Leu Leu Phe 260 265 270 Ile Glu Leu Gly Gly Gln Asn Leu Leu Ile Thr Asn Pro Arg Asp Ile 275 280 285 Pro Gly Leu Val Lys Glu Leu Ala Lys Tyr Pro Phe Thr Ala Ile Thr 290 295 300 Gly Val Asn Thr Leu Phe Asn Ala Leu Leu Asn Asn Lys Glu Phe Gln305 310 315 320 Gln Leu Asp Phe Ser Ser Leu His Leu Ser Ala Gly Gly Gly Met Pro 325 330 335 Val Gln Gln Val Val Ala Glu Arg Trp Val Lys Leu Thr Gly Gln Tyr 340 345 350 Leu Leu Glu Gly Tyr Gly Leu Thr Glu Cys Ala Pro Leu Val Ser Val 355 360 365 Asn Pro Tyr Asp Ile Asp Tyr His Ser Gly Ser Ile Gly Leu Pro Val 370 375 380 Pro Ser Thr Glu Ala Lys Leu Val Asp Asp Asp Asp Asn Glu Val Pro385 390 395 400 Pro Gly Gln Pro Gly Glu Leu Cys Val Lys Gly Pro Gln Val Met Leu 405 410 415 Gly Tyr Trp Gln Arg Pro Asp Ala Thr Asp Glu Ile Ile Lys Asn Gly 420 425 430 Trp Leu His Thr Gly Asp Ile Ala Val Met Asp Glu Glu Gly Phe Leu 435 440 445 Arg Ile Val Asp Arg Lys Lys Asp Met Ile Leu Val Ser Gly Phe Asn 450 455 460 Val Tyr Pro Asn Glu Ile Glu Asp Val Val Met Gln His Pro Gly Val465 470 475 480 Gln Glu Val Ala Ala Val Gly Val Pro Ser Gly Ser Ser Gly Glu Ala 485 490 495 Val Lys Ile Phe Val Val Lys Lys Asp Pro Ser Leu Thr Glu Glu Ser 500 505 510 Leu Val Thr Phe Cys Arg Arg Gln Leu Thr Gly Tyr Lys Val Pro Lys 515 520 525 Leu Val Glu Phe Arg Asp Glu Leu Pro Lys Ser Asn Val Gly Lys Ile 530 535 540 Leu Arg Arg Glu Leu Arg Asp Glu Ala Arg Gly Lys Val Asp Asn Lys545 550 555 560 Ala23515PRTCupriavidus necator 23Met His Pro His Ile His Ala Gln Arg Thr Pro Glu Lys Pro Ala Val1 5 10 15 Ile Met Gly Gly Ser Gly Ala Val Val Thr Tyr Arg Glu Leu Asp Glu 20 25 30 Arg Ser Asn Gln Val Ala His Leu Phe Arg Ser Gln Gly Leu Gln Pro 35 40 45 Gly Asp Arg Val Ala Phe Met Val Glu Asn His Pro Arg Leu Phe Glu 50 55 60 Leu Cys Trp Gly Ala Gln Arg Ser Gly Ile Val Tyr Val Cys Leu Ser65 70 75 80 Thr Arg Leu Asn Val Ala Asp Ala Ala His Ile Ile Asn Asp Ser Gly 85 90 95 Ala Arg Leu Leu Val Thr Thr His Ala Gln Ala Glu Val Ala Ala Ala 100 105 110 Leu Ala Gly Gln Thr Pro Ala Leu Arg Gly Arg Leu Met Leu Asp Gly 115 120 125 Thr Met Pro Gly Tyr Asp Ala Tyr Glu Thr Ala Leu Ala Arg Cys Pro 130 135 140 Ala Thr Arg Ile Asp Asp Glu Val Thr Gly Gly Asp Met Leu Tyr Ser145 150 155 160 Ser Gly Thr Thr Gly Arg Pro Lys Gly Val Tyr Ala Pro Pro Ser Ser 165 170 175 Pro Asn Ile Asp Asp Pro Thr Thr Leu Thr Ser Leu Cys Gln Arg Leu 180 185 190 Tyr Gly Phe Asp Ala Glu Thr Arg Tyr Leu Ser Pro Ala Pro Leu Tyr 195 200 205 His Ala Ala Pro Leu Arg Tyr Asn Met Thr Val Gln Ala Leu Gly Gly 210 215 220 Thr Ala Val Val Met Glu His Phe Asp Ala Glu His Tyr Leu Gln Leu225 230 235 240 Val Gln Gln His Arg Ile Thr His Thr Gln Leu Val Pro Thr Met Phe 245 250 255 Ser Arg Met Leu Lys Leu Pro Glu Ala Gln Arg Gln Ala Tyr Asp Val 260 265 270 Ser Ser Leu Arg Val Ala Ile His Ala Ala Ala Pro Cys Pro Val Gln 275 280 285 Val Lys Glu Ala Met Ile Ala Trp Trp Gly Pro Val Ile Trp Glu Tyr 290 295 300 Tyr Ala Gly Thr Glu Gly Asn Gly Val Thr Val Val Ser Thr Pro Glu305 310 315 320 Trp Leu Glu Arg Lys Gly Thr Val Gly Arg Ala Met Val Gly Lys Leu 325 330 335 Arg Ile Cys Gly Pro Asp Gly Ala Leu Leu Pro Pro Gly Glu Ser Gly 340 345 350 Thr Ile Tyr Phe Ala Glu Gly Arg Asp Phe Ser Tyr His Asn Asp Glu 355 360 365 Ala Lys Thr Ala Glu Ser Arg His Pro Gln Gln Pro Asp Trp Ser Thr 370 375 380 Ile Gly Asp Val Gly Tyr Val Asp Ala Asp Gly Tyr Leu Tyr Leu Thr385 390 395 400 Asp Arg Lys Ala Asn Met Ile Ile Ser Gly Gly Val Asn Ile Tyr Pro 405 410 415 Gln Glu Ala Glu Asn Leu Leu Met Thr His Pro Lys Val Met Asp Val 420 425 430 Ala Val Ile Gly Val Pro Asn Glu Asp Phe Gly Glu Glu Val Lys Ala 435 440 445 Val Val Gln Pro Val Asp Met Ser Gln Ala Gly Pro Glu Leu Ala Ala 450 455 460 Glu Leu Ile Ala Phe Cys Arg Ala Asn Leu Ser Ala Ile Lys Cys Pro465 470 475 480 Arg Ser Val Asp Phe Ala Ser Glu Leu Pro Arg Leu Pro Thr Gly Lys 485 490 495 Leu Leu Lys Arg Leu Leu Arg Asp Arg Tyr Trp Gly Gly His Ala Asn 500 505 510 Lys Leu Val 515 24320PRTAcidaminococcus fermentans 24Met Ser Lys Val Met Thr Leu Lys Asp Ala Ile Ala Lys Tyr Val His1 5 10 15 Ser Gly Asp His Ile Ala Leu Gly Gly Phe Thr Thr Asp Arg Lys Pro 20 25 30 Tyr Ala Ala Val Phe Glu Ile Leu Arg Gln Gly Ile Thr Asp Leu Thr 35 40 45 Gly Leu Gly Gly Ala Ala Gly Gly Asp Trp Asp Met Leu Ile Gly Asn 50 55 60 Gly Arg Val Lys Ala Tyr Ile Asn Cys Tyr Thr Ala Asn Ser Gly Val65 70 75 80 Thr Asn Val Ser Arg Arg Phe Arg Lys Trp Phe Glu Ala Gly Lys Leu 85 90 95 Thr Met Glu Asp Tyr Ser Gln Asp Val Ile Tyr Met Met Trp His Ala 100 105 110 Ala Ala Leu Gly Leu Pro Phe Leu Pro Val Thr Leu Met Gln Gly Ser 115 120 125 Gly Leu Thr Asp Glu Trp Gly Ile Ser Lys Glu Val Arg Lys Thr Leu 130 135 140 Asp Lys Val Pro Asp Asp Lys Phe Lys Tyr Ile Asp Asn Pro Phe Lys145 150 155 160 Pro Gly Glu Lys Val Val Ala Val Pro Val Pro Gln Val Asp Val Ala 165 170 175 Ile Ile His Ala Gln Gln Ala Ser Pro Asp Gly Thr Val Arg Ile Trp 180 185 190 Gly Gly Lys Phe Gln Asp Val Asp Ile Ala Glu Ala Ala Lys Tyr Thr 195 200 205 Ile Val Thr Cys Glu Glu Ile Ile Ser Asp Glu Glu Ile Arg Arg Asp 210 215 220 Pro Thr Lys Asn Asp Ile Pro Gly Met Cys Val Asp Ala Val Val Leu225 230 235 240 Ala Pro Tyr Gly Ala His Pro Ser Gln Cys Tyr Gly Leu Tyr Asp Tyr 245 250 255 Asp Asn Pro Phe Leu Lys Val Tyr Asp Lys Val Ser Lys Thr Gln Glu 260 265 270 Asp Phe Asp Ala Phe Cys Lys Glu Trp Val Phe Asp Leu Lys Asp His 275 280 285 Asp

Glu Tyr Leu Asn Lys Leu Gly Ala Thr Arg Leu Ile Asn Leu Lys 290 295 300 Val Val Pro Gly Leu Gly Tyr His Ile Asp Met Thr Lys Glu Asp Lys305 310 315 320 25266PRTAcidaminococcus fermentans 25Met Ala Asp Tyr Thr Asn Tyr Thr Asn Lys Glu Met Gln Ala Val Thr1 5 10 15 Ile Ala Lys Gln Ile Lys Asn Gly Gln Val Val Thr Val Gly Thr Gly 20 25 30 Leu Pro Leu Ile Gly Ala Ser Val Ala Lys Arg Val Tyr Ala Pro Asp 35 40 45 Cys His Ile Ile Val Glu Ser Gly Leu Met Asp Cys Ser Pro Val Glu 50 55 60 Val Pro Arg Ser Val Gly Asp Leu Arg Phe Met Ala His Cys Gly Cys65 70 75 80 Ile Trp Pro Asn Val Arg Phe Val Gly Phe Glu Ile Asn Glu Tyr Leu 85 90 95 His Lys Ala Asn Arg Leu Ile Ala Phe Ile Gly Gly Ala Gln Ile Asp 100 105 110 Pro Tyr Gly Asn Val Asn Ser Thr Ser Ile Gly Asp Tyr His His Pro 115 120 125 Lys Thr Arg Phe Thr Gly Ser Gly Gly Ala Asn Gly Ile Ala Thr Tyr 130 135 140 Ser Asn Thr Ile Ile Met Met Gln His Glu Lys Arg Arg Phe Met Asn145 150 155 160 Lys Ile Asp Tyr Val Thr Ser Pro Gly Trp Ile Asp Gly Pro Gly Gly 165 170 175 Arg Glu Arg Leu Gly Leu Pro Gly Asp Val Gly Pro Gln Leu Val Val 180 185 190 Thr Asp Lys Gly Ile Leu Lys Phe Asp Glu Lys Thr Lys Arg Met Tyr 195 200 205 Leu Ala Ala Tyr Tyr Pro Thr Ser Ser Pro Glu Asp Val Leu Glu Asn 210 215 220 Thr Gly Phe Asp Leu Asp Val Ser Lys Ala Val Glu Leu Glu Ala Pro225 230 235 240 Asp Pro Ala Val Ile Lys Leu Ile Arg Glu Glu Ile Asp Pro Gly Gln 245 250 255 Ala Phe Ile Gln Val Pro Thr Glu Ala Lys 260 265 26397PRTTreponema denticola 26Met Ile Val Lys Pro Met Val Arg Asn Asn Ile Cys Leu Asn Ala His1 5 10 15 Pro Gln Gly Cys Lys Lys Gly Val Glu Asp Gln Ile Glu Tyr Thr Lys 20 25 30 Lys Arg Ile Thr Ala Glu Val Lys Ala Gly Ala Lys Ala Pro Lys Asn 35 40 45 Val Leu Val Leu Gly Cys Ser Asn Gly Tyr Gly Leu Ala Ser Arg Ile 50 55 60 Thr Ala Ala Phe Gly Tyr Gly Ala Ala Thr Ile Gly Val Ser Phe Glu65 70 75 80 Lys Ala Gly Ser Glu Thr Lys Tyr Gly Thr Pro Gly Trp Tyr Asn Asn 85 90 95 Leu Ala Phe Asp Glu Ala Ala Lys Arg Glu Gly Leu Tyr Ser Val Thr 100 105 110 Ile Asp Gly Asp Ala Phe Ser Asp Glu Ile Lys Ala Gln Val Ile Glu 115 120 125 Glu Ala Lys Lys Lys Gly Ile Lys Phe Asp Leu Ile Val Tyr Ser Leu 130 135 140 Ala Ser Pro Val Arg Thr Asp Pro Asp Thr Gly Ile Met His Lys Ser145 150 155 160 Val Leu Lys Pro Phe Gly Lys Thr Phe Thr Gly Lys Thr Val Asp Pro 165 170 175 Phe Thr Gly Glu Leu Lys Glu Ile Ser Ala Glu Pro Ala Asn Asp Glu 180 185 190 Glu Ala Ala Ala Thr Val Lys Val Met Gly Gly Glu Asp Trp Glu Arg 195 200 205 Trp Ile Lys Gln Leu Ser Lys Glu Gly Leu Leu Glu Glu Gly Cys Ile 210 215 220 Thr Leu Ala Tyr Ser Tyr Ile Gly Pro Glu Ala Thr Gln Ala Leu Tyr225 230 235 240 Arg Lys Gly Thr Ile Gly Lys Ala Lys Glu His Leu Glu Ala Thr Ala 245 250 255 His Arg Leu Asn Lys Glu Asn Pro Ser Ile Arg Ala Phe Val Ser Val 260 265 270 Asn Lys Gly Leu Val Thr Arg Ala Ser Ala Val Ile Pro Val Ile Pro 275 280 285 Leu Tyr Leu Ala Ser Leu Phe Lys Val Met Lys Glu Lys Gly Asn His 290 295 300 Glu Gly Cys Ile Glu Gln Ile Thr Arg Leu Tyr Ala Glu Arg Leu Tyr305 310 315 320 Arg Lys Asp Gly Thr Ile Pro Val Asp Glu Glu Asn Arg Ile Arg Ile 325 330 335 Asp Asp Trp Glu Leu Glu Glu Asp Val Gln Lys Ala Val Ser Ala Leu 340 345 350 Met Glu Lys Val Thr Gly Glu Asn Ala Glu Ser Leu Thr Asp Leu Ala 355 360 365 Gly Tyr Arg His Asp Phe Leu Ala Ser Asn Gly Phe Asp Val Glu Gly 370 375 380 Ile Asn Tyr Glu Ala Glu Val Glu Arg Phe Asp Arg Ile385 390 395 27539PRTEuglena gracilis 27Met Ser Cys Pro Ala Ser Pro Ser Ala Ala Val Val Ser Ala Gly Ala1 5 10 15 Leu Cys Leu Cys Val Ala Thr Val Leu Leu Ala Thr Gly Ser Asn Pro 20 25 30 Thr Ala Leu Ser Thr Ala Ser Thr Arg Ser Pro Thr Ser Leu Val Arg 35 40 45 Gly Val Asp Arg Gly Leu Met Arg Pro Thr Thr Ala Ala Ala Leu Thr 50 55 60 Thr Met Arg Glu Val Pro Gln Met Ala Glu Gly Phe Ser Gly Glu Ala65 70 75 80 Thr Ser Ala Trp Ala Ala Ala Gly Pro Gln Trp Ala Ala Pro Leu Val 85 90 95 Ala Ala Ala Ser Ser Ala Leu Ala Leu Trp Trp Trp Ala Ala Arg Arg 100 105 110 Ser Val Arg Arg Pro Leu Ala Ala Leu Ala Glu Leu Pro Thr Ala Val 115 120 125 Thr His Leu Ala Pro Pro Met Ala Met Phe Thr Thr Thr Ala Lys Val 130 135 140 Ile Gln Pro Lys Ile Arg Gly Phe Ile Cys Thr Thr Thr His Pro Ile145 150 155 160 Gly Cys Glu Lys Arg Val Gln Glu Glu Ile Ala Tyr Ala Arg Ala His 165 170 175 Pro Pro Thr Ser Pro Gly Pro Lys Arg Val Leu Val Ile Gly Cys Ser 180 185 190 Thr Gly Tyr Gly Leu Ser Thr Arg Ile Thr Ala Ala Phe Gly Tyr Gln 195 200 205 Ala Ala Thr Leu Gly Val Phe Leu Ala Gly Pro Pro Thr Lys Gly Arg 210 215 220 Pro Ala Ala Ala Gly Trp Tyr Asn Thr Val Ala Phe Glu Lys Ala Ala225 230 235 240 Leu Glu Ala Gly Leu Tyr Ala Arg Ser Leu Asn Gly Asp Ala Phe Asp 245 250 255 Ser Thr Thr Lys Ala Arg Thr Val Glu Ala Ile Lys Arg Asp Leu Gly 260 265 270 Thr Val Asp Leu Val Val Tyr Ser Ile Ala Ala Pro Lys Arg Thr Asp 275 280 285 Pro Ala Thr Gly Val Leu His Lys Ala Cys Leu Lys Pro Ile Gly Ala 290 295 300 Thr Tyr Thr Asn Arg Thr Val Asn Thr Asp Lys Ala Glu Val Thr Asp305 310 315 320 Val Ser Ile Glu Pro Ala Ser Pro Glu Glu Ile Ala Asp Thr Val Lys 325 330 335 Val Met Gly Gly Glu Asp Trp Glu Leu Trp Ile Gln Ala Leu Ser Glu 340 345 350 Ala Gly Val Leu Ala Glu Gly Ala Lys Thr Val Ala Tyr Ser Tyr Ile 355 360 365 Gly Pro Glu Met Thr Trp Pro Val Tyr Trp Ser Gly Thr Ile Gly Glu 370 375 380 Ala Lys Lys Asp Val Glu Lys Ala Ala Lys Arg Ile Thr Gln Gln Tyr385 390 395 400 Gly Cys Pro Ala Tyr Pro Val Val Ala Lys Ala Leu Val Thr Gln Ala 405 410 415 Ser Ser Ala Ile Pro Val Val Pro Leu Tyr Ile Cys Leu Leu Tyr Arg 420 425 430 Val Met Lys Glu Lys Gly Thr His Glu Gly Cys Ile Glu Gln Met Val 435 440 445 Arg Leu Leu Thr Thr Lys Leu Tyr Pro Glu Asn Gly Ala Pro Ile Val 450 455 460 Asp Glu Ala Gly Arg Val Arg Val Asp Asp Trp Glu Met Ala Glu Asp465 470 475 480 Val Gln Gln Ala Val Lys Asp Leu Trp Ser Gln Val Ser Thr Ala Asn 485 490 495 Leu Lys Asp Ile Ser Asp Phe Ala Gly Tyr Gln Thr Glu Phe Leu Arg 500 505 510 Leu Phe Gly Phe Gly Ile Asp Gly Val Asp Tyr Asp Gln Pro Val Asp 515 520 525 Val Glu Ala Asp Leu Pro Ser Ala Ala Gln Gln 530 535 28398PRTPseudomonas reinekei MT1 28Met Lys Asn Ala Leu Ile Val Ser Pro Leu Arg Thr Pro Ile Gly Lys1 5 10 15 Phe Gly Gly Ala Leu Ala Pro Leu Thr Ala Glu His Leu Ala Ser Phe 20 25 30 Met Ile Ser Gln Val Met Ala Arg Thr Gly Val Pro Gly His Ser Leu 35 40 45 Asp Glu Val Ile Val Ala Gln Ser Tyr Ala Ser Ser Glu Ala Pro Cys 50 55 60 Ile Gly Arg Tyr Ala Ala Leu Ser Ala Gly Leu Pro Val Glu Val Pro65 70 75 80 Gly Tyr Thr Leu Asp Arg Arg Cys Gly Ser Gly Leu Gln Ala Val Ile 85 90 95 Asp Ala Ser Met Met Val Lys Thr Gly Asn Ala Glu Ala Val Leu Val 100 105 110 Val Gly Val Glu Ser Met Ser Asn Ile Glu Tyr Tyr Ser Thr Asp Met 115 120 125 Arg Trp Gly Ala Arg Ala Gly Ser Val Arg Phe His Asp Arg Leu Glu 130 135 140 Arg Gly Arg Glu Arg Ser Gln Pro Ser Glu Arg Phe Gly His Ile Ser145 150 155 160 Gly Met Pro Glu Thr Ala Asp Asn Leu Ala Leu Asp Tyr Gly Ile Ser 165 170 175 Arg Glu Glu Ala Asp Ser Phe Ser Val Arg Ser His Gln Asn Ala Ala 180 185 190 Ala Ala Trp Arg Glu Gly Arg Phe Ala Asp Glu Val Val Ala Val Asp 195 200 205 Val Pro Gly Lys Arg Gly Ala Val Thr Arg Val Thr Ile Asp Glu Gly 210 215 220 Ile Arg Glu Asp Ala Ser Leu Glu Ser Met Lys Ala Leu Arg Leu Ile225 230 235 240 Arg Pro Glu Gly Val Cys Thr Ala Gly Asn Ser Ser Gln Gln Asn Asp 245 250 255 Ala Ala Ala Gly Cys Leu Val Val Ser Pro Glu Tyr Ala Ala Arg His 260 265 270 Gly Leu Thr Pro Met Ala Arg Leu Val Asp Trp Ala Ala Ala Gly Cys 275 280 285 Glu Pro Ser Arg Met Gly Ile Gly Pro Val Pro Ala Thr Gln Lys Leu 290 295 300 Leu Met Arg Thr Gly Leu Ser Leu Ala Glu Leu Asp Leu Ile Glu Leu305 310 315 320 Asn Glu Ala Phe Ala Ala Gln Ala Leu Ala Val Leu Lys Thr Trp Gly 325 330 335 Leu Asp Asp Leu Ser Arg Val Asn Val Asn Gly Ser Gly Ile Ser Leu 340 345 350 Gly His Pro Ile Gly Ala Thr Gly Val Arg Ile Met Thr Thr Leu Leu 355 360 365 His Glu Met Arg Arg Arg Glu Ala Arg Tyr Gly Leu Glu Thr Met Cys 370 375 380 Ile Gly Gly Gly Gln Gly Leu Ala Ala Leu Phe Glu Arg Val385 390 395 29400PRTPseudomonas putida 29Met Arg Asp Val Phe Ile Cys Asp Ala Ile Arg Thr Pro Ile Gly Arg1 5 10 15 Phe Gly Gly Ala Leu Ala Gly Val Arg Ala Asp Asp Leu Ala Ala Val 20 25 30 Pro Leu Lys Ala Leu Ile Glu Pro Asn Pro Ala Val Gln Trp Asp Gln 35 40 45 Val Asp Glu Val Phe Phe Gly Cys Ala Asn Gln Ala Gly Glu Asp Asn 50 55 60 Arg Asn Val Ala Arg Met Ala Leu Leu Leu Ala Gly Leu Pro Glu Ser65 70 75 80 Ile Pro Gly Val Thr Leu Asn Arg Leu Cys Ala Ser Gly Met Asp Ala 85 90 95 Ile Gly Thr Ala Phe Arg Ala Ile Ala Ser Gly Glu Met Glu Leu Ala 100 105 110 Ile Ala Gly Gly Val Glu Ser Met Ser Arg Ala Pro Phe Val Met Gly 115 120 125 Lys Ala Glu Ser Gly Tyr Ser Arg Asn Met Lys Leu Glu Asp Thr Thr 130 135 140 Ile Gly Trp Arg Phe Ile Asn Pro Leu Met Lys Ser Gln Tyr Gly Val145 150 155 160 Asp Ser Met Pro Glu Thr Ala Asp Asn Val Ala Asp Asp Tyr Gln Val 165 170 175 Ser Arg Ala Asp Gln Asp Ala Phe Ala Leu Arg Ser Gln Gln Lys Ala 180 185 190 Ala Ala Ala Gln Ala Ala Gly Phe Phe Ala Glu Glu Ile Val Pro Val 195 200 205 Arg Ile Ala His Lys Lys Gly Glu Thr Ile Val Glu Arg Asp Glu His 210 215 220 Leu Arg Pro Glu Thr Thr Leu Glu Ala Leu Thr Lys Leu Lys Pro Val225 230 235 240 Asn Gly Pro Asp Lys Thr Val Thr Ala Gly Asn Ala Ser Gly Val Asn 245 250 255 Asp Gly Ala Ala Ala Leu Ile Leu Ala Ser Ala Glu Ala Val Lys Lys 260 265 270 His Gly Leu Thr Pro Arg Ala Arg Val Leu Gly Met Ala Ser Gly Gly 275 280 285 Val Ala Pro Arg Val Met Gly Ile Gly Pro Val Pro Ala Val Arg Lys 290 295 300 Leu Thr Glu Arg Leu Gly Val Ala Val Ser Asp Phe Asp Val Ile Glu305 310 315 320 Leu Asn Glu Ala Phe Ala Ser Gln Gly Leu Ala Val Leu Arg Glu Leu 325 330 335 Gly Val Ala Asp Asp Ala Pro Gln Val Asn Pro Asn Gly Gly Ala Ile 340 345 350 Ala Leu Gly His Pro Leu Gly Met Ser Gly Ala Arg Leu Val Leu Thr 355 360 365 Ala Leu His Gln Leu Glu Lys Ser Gly Gly Arg Lys Gly Leu Ala Thr 370 375 380 Met Cys Val Gly Val Gly Gln Gly Leu Ala Leu Ala Ile Glu Arg Val385 390 395 400 30400PRTBurkholderia xenovorans 30Met Thr Glu Ala Phe Leu Cys Asp Ala Ile Arg Thr Pro Ile Gly Arg1 5 10 15 Tyr Ala Gly Ala Leu Ser Ser Val Arg Ala Asp Asp Leu Gly Ala Val 20 25 30 Pro Leu Lys Ala Leu Met Glu Arg Asn Lys Glu Val Asp Trp Asn Ala 35 40 45 Ile Asp Asp Val Ile Tyr Gly Cys Ala Asn Gln Ala Gly Glu Asp Asn 50 55 60 Arg Asn Val Ala Arg Met Ser Leu Leu Leu Ala Gly Leu Pro Gln Gly65 70 75 80 Val Pro Gly Thr Thr Val Asn Arg Leu Cys Gly Ser Gly Met Asp Ala 85 90 95 Val Gly Ile Ala Ala Arg Ala Ile Lys Ser Gly Glu Ala Ala Leu Met 100 105 110 Val Ala Gly Gly Val Glu Ser Met Ser Arg Ala Pro Phe Val Thr Gly 115 120 125 Lys Ala Thr Ser Ala Phe Ser Arg Gln Ala Glu Ile Tyr Asp Thr Thr 130 135 140 Ile Gly Trp Arg Phe Val Asn Pro Leu Met Lys Lys Leu Tyr Gly Val145 150 155 160 Asp Ser Met Pro Glu Thr Gly Glu Asn Val Ala Thr Asp Tyr Asn Ile 165 170 175 Ser Arg Ala Asp Gln Asp Ala Phe Ala Leu Arg Ser Gln Gln Lys Ala 180 185 190 Ala Arg Ala Gln Arg Asp Gly Thr Leu Ala Gln Glu Ile Val Gly Val 195 200 205 Thr Ile Ala Gln Lys Lys Gly Asp Pro Val Thr Val Ser Gln Asp Glu 210 215 220 His Pro Arg Glu Thr Ser Leu Asp Ala Leu Ala Lys Leu Lys Gly Val225 230 235 240 Val Arg Pro Asp Gly Thr Val Thr Ala Gly Asn Ala Ser Gly Val Asn 245 250

255 Asp Gly Ala Ala Ala Leu Leu Leu Ala Asn Glu Glu Thr Ala Arg Arg 260 265 270 Phe Gly Leu Thr Pro Arg Ala Arg Val Leu Gly Ile Ala Thr Ala Gly 275 280 285 Val Ala Pro Arg Val Met Gly Ile Gly Pro Ala Pro Ala Thr Gln Lys 290 295 300 Leu Leu Ala Arg Leu Asn Met Ser Leu Asp Gln Phe Asp Val Ile Glu305 310 315 320 Leu Asn Glu Ala Phe Ala Ser Gln Gly Ile Ala Val Leu Arg Ala Leu 325 330 335 Gly Val Ala Asp Asp Asp Thr Arg Val Asn Pro Asn Gly Gly Ala Ile 340 345 350 Ala Leu Gly His Pro Leu Gly Met Ser Gly Ala Arg Leu Val Thr Thr 355 360 365 Ala Met Tyr Gln Leu His Arg Thr Gln Gly Arg Phe Ala Leu Cys Thr 370 375 380 Met Cys Ile Gly Val Gly Gln Gly Ile Ala Ile Ala Ile Glu Arg Val385 390 395 400 31456PRTArthrobacter sp. 31Met Ser Phe Asn Gly Gln Ser Ala Thr Gly Pro Asp Glu Ser Ala Ala1 5 10 15 Ala Pro Ala Ala Thr Pro Gly Ala Gly Leu Leu Arg Lys Ala Val Val 20 25 30 Val Gly Gly Asn Arg Ile Pro Phe Ala Arg Thr Gly Gly Ala Tyr Thr 35 40 45 Lys Ser Ser Asn Gln Asp Met Leu Thr Ala Ala Leu Asp Gly Leu Ile 50 55 60 Ala Arg Phe Gly Leu Ala Asp Glu Arg Ile Gly Glu Val Ala Ala Gly65 70 75 80 Ala Val Leu Lys His Ser Arg Asp Phe Asn Leu Thr Arg Glu Ala Val 85 90 95 Leu Gly Ser Ala Leu Ser Ala Glu Thr Pro Ala Tyr Asp Leu Gln Gln 100 105 110 Ala Cys Ala Thr Gly Leu Glu Thr Val Leu Gly Leu Ala Asn Lys Ile 115 120 125 Lys Leu Gly Gln Ile Asp Ser Ala Ile Ala Gly Gly Val Asp Ser Ala 130 135 140 Ser Asp Ala Pro Ile Ala Val Ser Glu Gly Leu Arg Glu Val Leu Leu145 150 155 160 Asp Leu Asn Arg Ala Lys Thr Leu Pro Gln Arg Leu Lys Val Leu Gly 165 170 175 Arg Leu Arg Pro Lys Asp Leu Ala Pro Asp Ala Pro Asn Thr Gly Glu 180 185 190 Pro Arg Thr Gly Leu Ser Met Gly Glu His Gln Ala Leu Thr Thr Ala 195 200 205 Gln Trp Lys Ile Thr Arg Glu Ala Gln Asp Glu Leu Ala Tyr Asn Ser 210 215 220 His Arg Asn Leu Ala Ala Ala Tyr Asp Ala Gly Phe Phe Asp Asp Leu225 230 235 240 Leu Thr Pro Tyr Arg Gly Leu Asn Arg Asp Ser Asn Leu Arg Ala Asp 245 250 255 Thr Thr Arg Glu Lys Leu Ser Thr Leu Lys Pro Val Phe Gly Lys Asn 260 265 270 Leu Gly Ala Glu Ala Thr Met Thr Ala Gly Asn Ser Thr Pro Leu Thr 275 280 285 Asp Gly Ala Ser Thr Val Leu Leu Ala Ser Glu Glu Trp Ala Asp Ala 290 295 300 His Glu Leu Pro Lys Leu Ala Thr Val Val Asp Gly Glu Ala Ala Ala305 310 315 320 Val Asp Phe Val His Gly Lys Asp Gly Leu Leu Met Ala Pro Ala Phe 325 330 335 Ala Val Pro Arg Leu Leu Ala Arg Asn Gly Leu Thr Leu Asp Asp Ile 340 345 350 Asp Phe Phe Glu Ile His Glu Ala Phe Ala Gly Thr Val Leu Ser Thr 355 360 365 Leu Ala Ala Trp Glu Asp Glu Glu Phe Gly Arg Thr Arg Leu Gly Leu 370 375 380 Asp Gly Pro Leu Gly Ser Ile Asp Arg Ala Lys Leu Asn Val Asn Gly385 390 395 400 Ser Ser Leu Ala Ala Gly His Pro Phe Ala Ala Thr Gly Gly Arg Ile 405 410 415 Val Ala Thr Leu Ala Lys Met Leu His Asp Lys Gly Gln Val Asp Gly 420 425 430 Arg Pro Ala Arg Gly Leu Ile Ser Ile Cys Ala Ala Gly Gly Gln Gly 435 440 445 Val Val Ala Ile Leu Glu Ala Ser 450 455 32394PRTBurkholderia xenovorans 32Met Thr Arg Asp Thr Arg Asp Val Val Ile Val Asp Ala Val Arg Thr1 5 10 15 Pro Ile Gly Lys Phe Arg Gly Ala Leu Ala Gly Val Arg Ala Asp His 20 25 30 Leu Gly Ala Leu Val Ile Asp Glu Leu Ile Arg Arg Ala Gly Val Lys 35 40 45 Pro Gln Ala Val Asn Asp Val Val Phe Gly Cys Val Thr Gln Ile Gly 50 55 60 Glu Gln Ser Ala Asn Ile Ala Arg Thr Ser Val Leu Gly Ala Gly Trp65 70 75 80 Pro Glu Thr Ile Pro Gly Leu Thr Ile Asp Arg Lys Cys Gly Ser Gly 85 90 95 Glu Glu Ala Val His Ile Ala Ala Gly Leu Ile Ala Phe Gly Ala Ala 100 105 110 Asp Val Ile Val Ala Gly Gly Ala Glu Ser Met Ser Arg Val Pro Met 115 120 125 Gly Ser Asn Arg Asp Leu His Gly Glu Ala Phe Gly Trp Met Ala Ser 130 135 140 Glu Arg Phe Glu Leu Thr Ser Gln Gly Glu Ala Ala Glu Arg Leu Cys145 150 155 160 Asp Cys Trp Ala Leu Thr Arg Ala Gln Leu Asp Ala Tyr Ser Val Glu 165 170 175 Ser His Arg Arg Ala Ala Ala Ala Ala Ala Glu Gly Trp Phe Ala Arg 180 185 190 Glu Ile Val Pro Val Pro Val Gly Gln Val Arg Glu Lys Ser Leu Glu 195 200 205 Gly Glu Ala Ala Leu Phe Ala Ala Asp Glu Thr Ile Arg Pro Gly Thr 210 215 220 Asn Ala Asp Lys Leu Ala Thr Leu Lys Ser Ser Phe Arg Ser Asp Gly225 230 235 240 Arg Leu Thr Ala Gly Asn Ser Ser Gln Ile Ser Asp Gly Ala Ala Ala 245 250 255 Leu Leu Leu Met Ser Ser Asp Lys Ala Arg Glu Leu Gly Val Lys Ala 260 265 270 Arg Ala Arg Val Arg Ala Val Thr Thr Val Gly Ser Asp Pro Thr Leu 275 280 285 Met Leu Thr Gly Pro Ile Leu Ala Thr Cys Gln Val Leu Glu Lys Ala 290 295 300 Gly Leu Gly Leu Ser Asp Ile Asp Leu Phe Glu Ile Asn Glu Ala Phe305 310 315 320 Ala Pro Val Pro Leu Val Trp Met Lys Glu Phe Gly Val Pro His Ala 325 330 335 Lys Leu Asn Val Asn Gly Gly Ala Ile Ala Leu Gly His Pro Leu Gly 340 345 350 Ala Ser Gly Ala Arg Ile Met Thr Ser Met Leu His Glu Leu Glu Arg 355 360 365 Arg Gly Ala Arg Tyr Gly Leu Gln Ala Ile Cys Cys Ala Gly Gly Met 370 375 380 Gly Thr Ala Thr Leu Ile Glu Arg Leu Asp385 390 33382PRTGeobacillus kaustophilus 33Met Arg Glu Ala Val Ile Val Glu Ala Val Arg Thr Pro Val Gly Lys1 5 10 15 Arg Asn Gly Val Phe Arg Asp Val His Pro Val His Leu Ala Ala Val 20 25 30 Val Leu Asp Glu Val Val Arg Arg Ala Gly Met Asp Lys Gly Ala Val 35 40 45 Glu Asp Ile Val Met Gly Cys Val Thr Pro Val Ala Glu Gln Gly Tyr 50 55 60 Asn Ile Gly Arg Leu Ala Ala Leu Glu Ala Gly Phe Pro Ile Glu Val65 70 75 80 Pro Ala Val Gln Ile Asn Arg Met Cys Gly Ser Gly Gln Gln Ala Ile 85 90 95 His Phe Ala Ala Gln Glu Ile Arg Ser Gly Asp Met Asp Val Thr Ile 100 105 110 Ala Ala Gly Val Glu Ser Met Thr Lys Val Pro Ile Leu Ser Asp Gly 115 120 125 Asn Glu Arg Thr Ile Pro Pro Ser Leu His Glu Lys Tyr Glu Phe Ile 130 135 140 His Gln Gly Val Ser Ala Glu Arg Ile Ala Lys Lys Tyr Gly Leu Thr145 150 155 160 Arg Glu Glu Leu Asp Ala Tyr Ala Tyr Glu Ser His Gln Arg Ala Leu 165 170 175 Ala Ala Leu Arg Glu Gly Lys Phe Arg Ala Glu Ile Val Pro Val Lys 180 185 190 Gly Leu Asp Arg Asp Gly Arg Glu Ile Leu Val Thr Asp Asp Glu Gly 195 200 205 Pro Arg Ala Asp Thr Ser Pro Glu Ala Leu Ala Ala Leu Lys Pro Val 210 215 220 Phe Gln Glu Asp Gly Leu Ile Thr Ala Gly Asn Ala Ser Gln Met Ser225 230 235 240 Asp Gly Ala Ala Ala Val Leu Leu Met Glu Arg Glu Ala Ala Arg Arg 245 250 255 Phe Gly Leu Lys Pro Lys Ala Arg Ile Val Ala Gln Thr Val Val Gly 260 265 270 Ser Asp Pro Thr Tyr Met Leu Asp Gly Val Ile Pro Ala Thr Arg Gln 275 280 285 Val Leu Lys Lys Ala Gly Leu Ser Ile Asp Asp Ile Asp Leu Ile Glu 290 295 300 Ile Asn Glu Ala Phe Ala Pro Val Val Leu Ala Trp Gln Lys Glu Ile305 310 315 320 Gly Ala Pro Leu Glu Lys Val Asn Val Asn Gly Gly Ala Ile Ala Leu 325 330 335 Gly His Pro Leu Gly Ala Thr Gly Ala Lys Leu Met Thr Ser Leu Val 340 345 350 His Glu Leu Glu Arg Arg Gly Gly Arg Tyr Gly Leu Leu Thr Ile Cys 355 360 365 Ile Gly His Gly Met Ala Thr Ala Thr Ile Ile Glu Arg Glu 370 375 380 34415PRTGordonia bronchialis 34Met Ala Pro Cys Ser Val Lys Ala Met Pro Glu Ala Val Ile Val Ala1 5 10 15 His Ala Arg Ser Pro Ile Gly Arg Ala Gly Lys Gly Ser Leu Lys Asp 20 25 30 Val Arg Pro Asp Glu Leu Ser Arg Gln Met Val Ala Ala Ala Leu Ala 35 40 45 Lys Val Pro Glu Leu Ala Pro Ser Asp Ile Glu Asp Ile His Trp Gly 50 55 60 Ile Gly Gln Pro Gly Gly Gln Gly Gly Tyr Asn Ile Ala Arg Val Ile65 70 75 80 Ala Val Glu Leu Gly Tyr Asp His Ile Pro Gly Val Thr Val Asn Arg 85 90 95 Tyr Cys Ser Ser Ser Leu Gln Thr Thr Arg Met Ala Leu His Ala Ile 100 105 110 Lys Ala Gly Glu Ala Asp Val Leu Ile Ser Gly Gly Val Glu Ser Val 115 120 125 Ser Ser Phe Gly Ile Ser Gly Gly Ala Asp Gly Ala Pro Asp Ser Lys 130 135 140 Asn Pro Val Phe Asp Asp Ala Gln Ala Arg Thr Ala Lys Ala Ala Glu145 150 155 160 Gly Gly Ala Pro Ala Trp Thr Asp Pro Arg Glu Gln Gly Leu Ile Pro 165 170 175 Asp Val Tyr Ile Ala Met Gly Gln Thr Ala Glu Asn Val Ala Ser Phe 180 185 190 Thr Gly Ile Ser Arg Glu Asp Gln Asp Arg Trp Ser Val Leu Ser Gln 195 200 205 Asn Arg Ala Glu Glu Ala Ile Asn Ala Gly Phe Phe Glu Arg Glu Ile 210 215 220 Asp Pro Val Thr Leu Pro Asp Gly Ser Thr Val Asn Thr Asp Asp Gly225 230 235 240 Pro Arg Ala Gly Thr Thr Tyr Glu Lys Val Ser Gln Leu Lys Pro Val 245 250 255 Phe Arg Pro Asp Gly Thr Val Thr Ala Gly Asn Ala Cys Pro Leu Asn 260 265 270 Asp Gly Ala Ala Ala Leu Val Ile Met Ser Asp Ser Lys Ala Lys Gln 275 280 285 Leu Gly Leu Thr Pro Leu Ala Arg Val Val Ala Thr Ala Ala Thr Gly 290 295 300 Leu Ser Pro Glu Ile Met Gly Leu Gly Pro Ile Glu Ala Ile Arg Lys305 310 315 320 Val Leu Arg Ile Ser Gly Met Ser Leu Ser Asp Ile Asp Leu Val Glu 325 330 335 Ile Asn Glu Ala Phe Ala Val Gln Val Leu Gly Ser Ala Asn Glu Leu 340 345 350 Gly Ile Asp His Asp Lys Leu Asn Val Ser Gly Gly Ala Ile Ala Leu 355 360 365 Gly His Pro Phe Gly Met Thr Gly Ala Arg Ile Thr Thr Thr Leu Leu 370 375 380 Asn Asn Leu Gln Thr Arg Asp Lys Thr Phe Gly Ile Glu Ser Met Cys385 390 395 400 Val Gly Gly Gly Gln Gly Met Ala Met Val Leu Glu Arg Leu Ser 405 410 415 35387PRTCitrobacter freundii 35Met Glu Gln Val Val Ile Val Asp Ala Ile Arg Thr Pro Met Gly Arg1 5 10 15 Ser Lys Gly Gly Ala Phe Arg Asn Val Arg Ala Glu Asp Leu Ser Ala 20 25 30 His Leu Met Arg Ser Leu Leu Ala Arg Asn Pro Ala Leu Asp Pro Thr 35 40 45 Ala Leu Asp Asp Ile Tyr Trp Gly Cys Val Gln Gln Thr Leu Glu Gln 50 55 60 Gly Phe Asn Ile Ala Arg Asn Ala Ala Leu Leu Ala Glu Ile Pro His65 70 75 80 Ser Val Pro Ala Val Thr Val Asn Arg Leu Cys Gly Ser Ser Met Gln 85 90 95 Ala Leu His Asp Ala Ala Arg Met Ile Met Thr Gly Asp Ala Gln Ala 100 105 110 Cys Leu Ile Gly Gly Val Glu His Met Gly His Val Pro Met Ser His 115 120 125 Gly Val Asp Phe His Pro Gly Met Ser Arg Asn Val Ala Lys Ala Ala 130 135 140 Gly Met Met Gly Leu Thr Ala Glu Met Leu Ser Arg Met His Gly Ile145 150 155 160 Ser Arg Glu Met Gln Asp Ala Phe Ala Ala Arg Ser His Ala Arg Ala 165 170 175 Trp Ala Ala Thr Gln Ser Gly Ala Phe Lys Asn Glu Ile Ile Pro Thr 180 185 190 Gly Gly His Asp Ala Asp Gly Val Leu Lys Gln Phe Asn Tyr Asp Glu 195 200 205 Val Ile Arg Pro Glu Thr Thr Val Glu Ala Leu Ser Thr Leu Arg Pro 210 215 220 Ala Phe Asp Pro Val Ser Gly Thr Val Thr Ala Gly Thr Ser Ser Ala225 230 235 240 Leu Ser Asp Gly Ala Ala Ala Met Leu Val Met Ser Glu Ser Arg Ala 245 250 255 Arg Glu Leu Gly Leu Thr Pro Arg Ala Arg Ile Arg Ser Met Ala Val 260 265 270 Val Gly Cys Asp Pro Ser Ile Met Gly Tyr Gly Pro Val Pro Ala Ser 275 280 285 Lys Leu Ala Leu Lys Lys Ala Gly Leu Ser Thr Ser Asp Ile Gly Leu 290 295 300 Phe Glu Met Asn Glu Ala Phe Ala Ala Gln Ile Leu Pro Cys Ile Lys305 310 315 320 Asp Leu Gly Leu Met Glu Gln Ile Asp Glu Lys Ile Asn Leu Asn Gly 325 330 335 Gly Ala Ile Ala Leu Gly His Pro Leu Gly Cys Ser Gly Ala Arg Ile 340 345 350 Ser Thr Thr Leu Leu Asn Leu Met Glu Arg Lys Asp Val Gln Phe Gly 355 360 365 Leu Ala Thr Met Cys Ile Gly Leu Gly Gln Gly Ile Ala Thr Val Phe 370 375 380 Glu Arg Val385 36393PRTBurkholderia sp. 36Met Arg Glu Ala Val Ile Val Ser Thr Ala Arg Thr Pro Leu Thr Lys1 5 10 15 Ala His Arg Gly Glu Phe Asn Ile Thr Pro Gly Pro Thr Leu Ala Ser 20 25 30 Phe Ala Val Arg Ala Ala Val Glu Arg Ser Gly Val Asp Pro Asp Ile 35 40 45 Ile Glu Asp Ala Ile Leu Gly Cys Gly Tyr Pro Glu Gly Thr Thr Gly 50 55 60 Arg Asn Val Ala Arg Gln Ser Val Ile Arg Ala Gly Leu Pro Leu Ser65 70 75 80 Ile Ala Gly Thr Thr Val Asn Arg Phe Cys Ala Ser Gly Leu Gln Ala 85 90 95 Ile Ala Met Ala Ala Gly Arg Ile Val Val Asp Gly Ala Pro Ala Met

100 105 110 Ile Ala Gly Gly Val Glu Ser Ile Ser Asn Ile Gln Thr Arg Glu Asp 115 120 125 Gly Val Ser Gly Leu Asp Pro Trp Ile Val Glu His Lys Pro Ser Leu 130 135 140 Tyr Thr Ala Met Ile Asp Thr Ala Asp Ile Val Ala Arg Arg Tyr Gly145 150 155 160 Ile Ser Arg Glu Ala Gln Asp Gln Phe Ser Val Glu Ser Gln Arg Arg 165 170 175 Thr Ala Glu Ala Gln Gln Ala Gly Arg Tyr Ala Asp Glu Ile Ile Pro 180 185 190 Val Thr Thr Thr Met Ala Ile Thr Asp Lys Glu Thr Arg Ala Val Ser 195 200 205 Tyr Arg Glu Val Thr Val Ser Ala Asp Asn Cys Asn Arg Pro Gly Thr 210 215 220 Thr Tyr Glu Ala Leu Ala Lys Leu Ala Pro Val Lys Gly Pro Asp Gln225 230 235 240 Phe Ile Thr Ala Gly Asn Ala Ser Gln Asn Ala Asp Gly Ala Ser Ala 245 250 255 Cys Val Leu Met Glu Ala Lys Ala Ala Glu Arg Ala Asn Phe Ala Pro 260 265 270 Leu Gly Ala Phe Arg Gly Leu Ala Leu Ala Gly Cys Glu Pro Asp Glu 275 280 285 Met Gly Ile Gly Pro Val Leu Ala Val Pro Lys Leu Leu Ala Arg His 290 295 300 Gly Leu Thr Val Asp Asp Ile Gly Leu Trp Glu Leu Asn Glu Ala Phe305 310 315 320 Ala Ser Gln Ala Val Tyr Cys Gln Lys Arg Leu Glu Ile Pro Ser Glu 325 330 335 Arg Leu Asn Val Asn Gly Gly Ala Ile Ser Ile Gly His Pro Phe Gly 340 345 350 Met Thr Gly Ser Arg Leu Val Gly His Val Leu Ile Glu Gly Arg Arg 355 360 365 Arg Gly Val Lys Tyr Ala Val Val Thr Met Cys Met Ala Gly Gly Met 370 375 380 Gly Ala Ala Gly Leu Phe Glu Ile Tyr385 390 37378PRTBeijerinckia indica 37Met Thr Lys Val Val Ile Ala Gly Tyr Ile Arg Ser Pro Phe Thr Leu1 5 10 15 Ala Lys Lys Gly Glu Leu Ala Thr Val Arg Pro Asp Asp Leu Ala Ala 20 25 30 Gln Val Val Lys Gly Leu Ile Lys Lys Thr Gly Ile Pro Ala Glu Asp 35 40 45 Ile Glu Asp Leu Leu Leu Gly Cys Ala Phe Pro Glu Gly Glu Gln Gly 50 55 60 Phe Asn Val Ala Arg Leu Val Ser Phe Leu Ala Gly Leu Pro Leu Ser65 70 75 80 Val Gly Ala Ser Thr Val Asn Arg Phe Cys Gly Ser Ser Met Thr Thr 85 90 95 Val His Met Ala Ala Gly Ala Ile Gln Met Asn Ala Gly Asn Ala Phe 100 105 110 Ile Ala Ala Gly Val Glu Ser Met Ser Arg Val Pro Met Met Gly Phe 115 120 125 Asn Pro Leu Pro Asn Pro Glu Leu Ala Ala Thr Met Pro Gly Ala Tyr 130 135 140 Met Gly Met Gly Asp Thr Ala Glu Asn Val Ala Ala Lys Trp Thr Ile145 150 155 160 Ser Arg Lys Glu Gln Glu Glu Phe Ala Leu Arg Ser His Gln Arg Ala 165 170 175 Thr Ala Ala Gln Lys Glu Gly Arg Leu Thr Gly Glu Ile Ile Pro Ile 180 185 190 Thr Gly Arg Lys Gly Thr Ile Thr Thr Asp Gly Cys Ile Arg Pro Asp 195 200 205 Thr Thr Leu Glu Gly Leu Ala Glu Leu Lys Pro Ala Phe Ser Ala Asn 210 215 220 Gly Val Val Thr Ala Gly Thr Ser Ser Pro Leu Thr Asp Gly Ala Ala225 230 235 240 Ala Val Leu Val Cys Ser Glu Asp Tyr Ala Lys His His His Leu Asp 245 250 255 Val Leu Ala Ser Val Lys Ala Ile Ala Val Ser Gly Cys Ser Pro Glu 260 265 270 Ile Met Gly Ile Gly Pro Val Ala Ala Ser Arg Lys Ala Leu Ala Arg 275 280 285 Ala Gly Leu Glu Ala Gly Gln Ile Asp Ile Val Glu Leu Asn Glu Ala 290 295 300 Phe Ala Ser Gln Ser Ile Ala Cys Met Arg Glu Leu Asn Leu Ser Pro305 310 315 320 Asp Arg Val Asn Ile Asp Gly Gly Ala Ile Ala Leu Gly His Pro Leu 325 330 335 Gly Ala Thr Gly Ala Arg Ile Val Gly Lys Ala Ala Ser Leu Leu Lys 340 345 350 Arg Glu Lys Gly Lys Tyr Ala Leu Ala Thr Gln Cys Ile Gly Gly Gly 355 360 365 Gln Gly Ile Ala Thr Val Leu Glu Ala Phe 370 375 38403PRTArthrobacter arilaitensis 38Met Gln Gln Ala Tyr Leu Tyr Asp Ala Ile Arg Thr Pro Phe Gly Lys1 5 10 15 Ile Gly Gly Ala Leu Ser Ser His Arg Pro Asp Asp Leu Ala Ala His 20 25 30 Val Val Arg Glu Leu Val Ala Arg Ser Pro Lys Leu Asp Val Ala Asp 35 40 45 Ile Asp Glu Ser Ile Phe Gly Asn Ala Asn Gly Ala Gly Glu Glu Asn 50 55 60 Arg Asn Val Ala Arg Met Ala Thr Leu Leu Ala Gly Leu Pro Thr Ser65 70 75 80 Leu Pro Gly Thr Thr Met Asn Arg Leu Cys Gly Ser Ser Leu Asp Ala 85 90 95 Ser Ile Ala Ala Ser Arg Gln Ile Ala Thr Gly Asp Ala Asp Leu Val 100 105 110 Leu Val Gly Gly Val Glu Ser Met Ser Arg Ala Pro Trp Val Leu Pro 115 120 125 Lys Thr Glu Arg Pro Phe Pro Met Ser Asn Leu Glu Leu Ala Asn Thr 130 135 140 Thr Leu Gly Trp Arg Leu Val Asn Pro Ala Met Pro Gly Glu Trp Thr145 150 155 160 Val Ser Leu Gly Glu Ala Thr Glu Gln Leu Arg Glu Lys His Gly Ile 165 170 175 Ser Arg Glu Asp Gln Asp Glu Phe Ser Ala Ala Ser His Gln Arg Ala 180 185 190 Ala Ala Ala Trp Gln Ala Gly Lys Tyr Asp Asn Leu Val Val Pro Val 195 200 205 Pro Pro Ala Asn Lys Arg Gly Thr Glu Val Thr Arg Asp Glu Thr Ile 210 215 220 Arg Ala Asp Ser Thr Ala Gln Thr Leu Ser Lys Leu Arg Thr Val Phe225 230 235 240 Arg Thr Gly Glu Asn Ala Thr Val Thr Ala Gly Asn Ala Ser Pro Met 245 250 255 Ser Asp Gly Ala Ser Ala Ala Phe Ile Gly Ser Glu Arg Gly Gly Glu 260 265 270 Leu Leu Gly Ala Ala Pro Ile Ala Arg Ile Ala Ser Asn Gly Ala Ala 275 280 285 Ala Leu Asp Pro Gln Phe Phe Gly Phe Ala Pro Val Glu Ala Ala Asn 290 295 300 Lys Ala Leu Ala Lys Ala Gly Leu Lys Trp Ser Asp Ile Ala Ala Val305 310 315 320 Glu Leu Asn Glu Ala Phe Ala Ala Gln Ser Leu Ala Cys Ile Arg Ala 325 330 335 Trp Asp Ile Asp Pro Ala Ile Val Asn Ala Trp Gly Gly Ala Ile Ser 340 345 350 Ile Gly His Pro Leu Gly Ala Ser Gly Leu Arg Ile Leu Gly Thr Val 355 360 365 Ala Arg Arg Leu Ala Glu Ser Gly Glu Arg Tyr Gly Leu Ala Ala Ile 370 375 380 Cys Ile Gly Val Gly Gln Gly Leu Ala Val Val Val Glu Asn Ile Asn385 390 395 400 Ala Thr Lys39394PRTCupriavidus necator 39Met Thr Arg Glu Val Val Val Val Ser Gly Val Arg Thr Ala Ile Gly1 5 10 15 Thr Phe Gly Gly Ser Leu Lys Asp Val Ala Pro Ala Glu Leu Gly Ala 20 25 30 Leu Val Val Arg Glu Ala Leu Ala Arg Ala Gln Val Ser Gly Asp Asp 35 40 45 Val Gly His Val Val Phe Gly Asn Val Ile Gln Thr Glu Pro Arg Asp 50 55 60 Met Tyr Leu Gly Arg Val Ala Ala Val Asn Gly Gly Val Thr Ile Asn65 70 75 80 Ala Pro Ala Leu Thr Val Asn Arg Leu Cys Gly Ser Gly Leu Gln Ala 85 90 95 Ile Val Ser Ala Ala Gln Thr Ile Leu Leu Gly Asp Thr Asp Val Ala 100 105 110 Ile Gly Gly Gly Ala Glu Ser Met Ser Arg Ala Pro Tyr Leu Ala Pro 115 120 125 Ala Ala Arg Trp Gly Ala Arg Met Gly Asp Ala Gly Leu Val Asp Met 130 135 140 Met Leu Gly Ala Leu His Asp Pro Phe His Arg Ile His Met Gly Val145 150 155 160 Thr Ala Glu Asn Val Ala Lys Glu Tyr Asp Ile Ser Arg Ala Gln Gln 165 170 175 Asp Glu Ala Ala Leu Glu Ser His Arg Arg Ala Ser Ala Ala Ile Lys 180 185 190 Ala Gly Tyr Phe Lys Asp Gln Ile Val Pro Val Val Ser Lys Gly Arg 195 200 205 Lys Gly Asp Val Thr Phe Asp Thr Asp Glu His Val Arg His Asp Ala 210 215 220 Thr Ile Asp Asp Met Thr Lys Leu Arg Pro Val Phe Val Lys Glu Asn225 230 235 240 Gly Thr Val Thr Ala Gly Asn Ala Ser Gly Leu Asn Asp Ala Ala Ala 245 250 255 Ala Val Val Met Met Glu Arg Ala Glu Ala Glu Arg Arg Gly Leu Lys 260 265 270 Pro Leu Ala Arg Leu Val Ser Tyr Gly His Ala Gly Val Asp Pro Lys 275 280 285 Ala Met Gly Ile Gly Pro Val Pro Ala Thr Lys Ile Ala Leu Glu Arg 290 295 300 Ala Gly Leu Gln Val Ser Asp Leu Asp Val Ile Glu Ala Asn Glu Ala305 310 315 320 Phe Ala Ala Gln Ala Cys Ala Val Thr Lys Ala Leu Gly Leu Asp Pro 325 330 335 Ala Lys Val Asn Pro Asn Gly Ser Gly Ile Ser Leu Gly His Pro Ile 340 345 350 Gly Ala Thr Gly Ala Leu Ile Thr Val Lys Ala Leu His Glu Leu Asn 355 360 365 Arg Val Gln Gly Arg Tyr Ala Leu Val Thr Met Cys Ile Gly Gly Gly 370 375 380 Gln Gly Ile Ala Ala Ile Phe Glu Arg Ile385 390 40401PRTEscherichia coli 40Met Arg Glu Ala Phe Ile Cys Asp Gly Ile Arg Thr Pro Ile Gly Arg1 5 10 15 Tyr Gly Gly Ala Leu Ser Ser Val Arg Ala Asp Asp Leu Ala Ala Ile 20 25 30 Pro Leu Arg Glu Leu Leu Val Arg Asn Pro Arg Leu Asp Ala Glu Cys 35 40 45 Ile Asp Asp Val Ile Leu Gly Cys Ala Asn Gln Ala Gly Glu Asp Asn 50 55 60 Arg Asn Val Ala Arg Met Ala Thr Leu Leu Ala Gly Leu Pro Gln Ser65 70 75 80 Val Ser Gly Thr Thr Ile Asn Arg Leu Cys Gly Ser Gly Leu Asp Ala 85 90 95 Leu Gly Phe Ala Ala Arg Ala Ile Lys Ala Gly Asp Gly Asp Leu Leu 100 105 110 Ile Ala Gly Gly Val Glu Ser Met Ser Arg Ala Pro Phe Val Met Gly 115 120 125 Lys Ala Ala Ser Ala Phe Ser Arg Gln Ala Glu Met Phe Asp Thr Thr 130 135 140 Ile Gly Trp Arg Phe Val Asn Pro Leu Met Ala Gln Gln Phe Gly Thr145 150 155 160 Asp Ser Met Pro Glu Thr Ala Glu Asn Val Ala Glu Leu Leu Lys Ile 165 170 175 Ser Arg Glu Asp Gln Asp Ser Phe Ala Leu Arg Ser Gln Gln Arg Thr 180 185 190 Ala Lys Ala Gln Ser Ser Gly Ile Leu Ala Glu Glu Ile Val Pro Val 195 200 205 Val Leu Lys Asn Lys Lys Gly Val Val Thr Glu Ile Gln His Asp Glu 210 215 220 His Leu Arg Pro Glu Thr Thr Leu Glu Gln Leu Arg Gly Leu Lys Ala225 230 235 240 Pro Phe Arg Ala Asn Gly Val Ile Thr Ala Gly Asn Ala Ser Gly Val 245 250 255 Asn Asp Gly Ala Ala Ala Leu Ile Ile Ala Ser Glu Gln Met Ala Ala 260 265 270 Ala Gln Gly Leu Thr Pro Arg Ala Arg Ile Val Ala Met Ala Thr Ala 275 280 285 Gly Val Glu Pro Arg Leu Met Gly Leu Gly Pro Val Pro Ala Thr Arg 290 295 300 Arg Val Leu Glu Arg Ala Gly Leu Ser Ile His Asp Met Asp Val Ile305 310 315 320 Glu Leu Asn Glu Ala Phe Ala Ala Gln Ala Leu Gly Val Leu Arg Glu 325 330 335 Leu Gly Leu Pro Asp Asp Ala Pro His Val Asn Pro Asn Gly Gly Ala 340 345 350 Ile Ala Leu Gly His Pro Leu Gly Met Ser Gly Ala Arg Leu Ala Leu 355 360 365 Ala Ala Ser His Glu Leu His Arg Arg Asn Gly Arg Tyr Ala Leu Cys 370 375 380 Thr Met Cys Ile Gly Val Gly Gln Gly Ile Ala Met Ile Leu Glu Arg385 390 395 400 Val

Claims

1. A method of shielding a carbon chain aliphatic backbone, functionalized with terminal carboxyl groups, in a recombinant host, said method comprising: enzymatically converting a n-carboxy-2-enoic acid to a n-carboxy-2-enoate methyl ester in said host using a polypeptide having the activity of a fatty acid O-methyltransferase, wherein n+1 reflects length of the carbon chain aliphatic backbone; wherein when the n-carboxy-2-enoic acid is 2(E) heptenedioic acid, the method optionally further comprises enzymatically converting 2(E)-heptenedioate methyl ester to pimeloyl-CoA.

2. (canceled)

3. (canceled)

4. The method of claim 3, said method further comprising enzymatically converting pimeloyl-CoA to a product selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol; wherein. pimeloyl-CoA is converted to the product using one or more polypeptides having thioesterase, reversible CoA-ligase, glutaconate CoA-transferase, .omega.-transaminase, 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, alcohol dehydrogenase, carboxylate reductase or alcohol dehydrogenase activity.

5. (canceled)

6. A method of producing 2(E)-heptenedioyl-CoA methyl ester in a recombinant host, said method comprising: enzymatically converting 2(E)-heptenedioate to 2(E)-heptenedioate methyl ester using a polypeptide having fatty acid O-methyltransferase activity, said method optionally further comprising enzymatically converting 2(E)-heptenedioate methyl ester to pimeloyl-CoA methyl ester, wherein the 2(E)-heptenedioate is enzymatically produced from 2(E)-heptenedioyl-CoA using a polypeptide having thioesterase or CoA-transferase activity.

7. (canceled)

8. (canceled)

9. (canceled)

10. The method of claim 6, wherein: said polypeptide having thioesterase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 4 or SEQ ID NO: 5; said polypeptide having CoA-transferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24 or SEQ ID NO: 25; and said polypeptide having fatty acid O-methyltransferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.

11. (canceled)

12. The method of claim 1, wherein: the polypeptide having fatty acid O-methyltransferase activity is classified under EC 2.1.1.15; and the polypeptide having CoA ligase activity is classified under EC 6.2.1.2 or EC 6.2.1.3.

13. (canceled)

14. The method of claim 6, wherein 2(E)-heptenedioate methyl ester is enzymatically converted to 2(E)-heptenedioyl-CoA methyl ester using a polypeptide having CoA ligase activity classified under EC 6.2.1, the method optionally further comprising enzymatically converting 2(E)-heptenedioyl-CoA methyl ester to pimeloyl-CoA methyl ester using a polypeptide having trans-2-enoyl-CoA reductase activity; wherein the polypeptide having CoA ligase activity is classified under EC 6.2.1.2 or EC 6.2.1.3.

15. (canceled)

16. (canceled)

17. (canceled)

18. The method of claim 14, said method further comprising enzymatically converting pimeloyl-CoA methyl ester to pimeloyl-CoA using a polypeptide having pimelyl-[acp]methyl ester esterase activity, said polypeptide having at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 6.

19. (canceled)

20. (canceled)

21. The method of claim 18, further comprising enzymatically converting pimeloyl-CoA to a product selected from the group consisting of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol; wherein: pimeloyl-CoA is converted to pimelic acid using a polypeptide having thioesterase, reversible CoA-ligase, or glutaconate CoA-transferase activity; or pimeloyl-CoA is converted to pimelate semialdehyde using a polypeptide having acetylating aldehyde dehydrogenase activity.

22. (canceled)

23. The method of claim 21, wherein said method further comprises enzymatically converting pimelic acid to pimelate semialdehyde using a polypeptide having carboxylate reductase activity.

24. (canceled)

25. The method of claim 23, said method further comprising: enzymatically converting pimelate semialdehyde to pimelic acid using a polypeptide having 5-oxopentanoate dehydrogenase, 6-oxohexanoate dehydrogenase, 7-oxoheptanoate dehydrogenase, or aldehyde dehydrogenase activity; enzymatically converting pimelate semialdehyde to 7-aminoheptanoate using a polypeptide having .omega.-transaminase activity; enzymatically converting pimelate semialdehyde to heptamethylenediamine using a polypeptide having .omega.-transaminase and/or carboxylate reductase activity; or enzymatically converting pimelate semialdehyde to 7-hydroxyheptanoate using a polypeptide having 6-hydroxyhexanoate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, or alcohol dehydrogenase activity, wherein 7-hydroxyheptanoate is converted to 1,7-heptanediol using a polypeptide having carboxylate reductase and alcohol dehydrogenase activity.

26. (canceled)

27. (canceled)

28. (canceled)

29. (canceled)

30. The method of claim 1, wherein one or more steps of said method are performed by fermentation.

31. The method of claim 1, wherein said host is subjected to a cultivation strategy under aerobic, anaerobic, micro-aerobic, or mixed oxygen/denitrification cultivation conditions.

32. The method of claim 1, wherein said host is cultured under conditions of phosphate, oxygen, and/or nitrogen limitation.

33. The method of claim 1, wherein said host is retained using a ceramic membrane to maintain a high cell density during fermentation.

34. The method of claim 30, wherein the principal carbon source fed to the fermentation derives from biological or non-biological feedstocks; wherein the biological feedstock is, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid, formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste; and wherein the non-biological feedstock is, or derives from, natural gas, syngas, CO2/H2, methanol, ethanol, benzoate, non-volatile residue (NVR) caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

35. (canceled)

36. (canceled)

37. The method of claim 30, wherein said host comprises one or more polypeptides having attenuated polyhydroxyalkanoate synthase, acetyl-CoA thioesterase, acetyl-CoA specific .beta.-ketothiolase, phosphotransacetylase forming acetate, acetate kinase, lactate dehydrogenase, menaquinol-fumarate oxidoreductase, 2-oxoacid decarboxylase producing isobutanol, alcohol dehydrogenase forming ethanol, triose phosphate isomerase, pyruvate decarboxylase, glucose-6-phosphate isomerase, transhydrogenase dissipating the NADPH imbalance, glutamate dehydrogenase dissipating the NADPH imbalance, NADH/NADPH-utilizing glutamate dehydrogenase, pimeloyl-CoA dehydrogenase; acyl-CoA dehydrogenase accepting C7 building blocks and central precursors as substrates; glutaryl-CoA dehydrogenase; or pimeloyl-CoA synthetase activity, and optionally, wherein the host overexpresses one or more genes encoding a polypeptide having acetyl-CoA synthetase; 6-phosphogluconate dehydrogenase; transketolase; puridine nucleotide transhydrogenase; formate dehydrogenase; glyceraldehyde-3P-dehydrogenase; malic enzyme; glucose-6-phosphate dehydrogenase; fructose 1,6 diphosphatase; L-alanine dehydrogenase; PEP carboxylase, pyruvate carboxylase; PEP carboxykinase; PEP synthase; L-glutamate dehydrogenase specific to the NADPH used to generate a co-factor imbalance; methanol dehydrogenase, formaldehyde dehydrogenase, lysine transporter; dicarboxylate transporter; S-adenosylmethionine synthetase; 3-phosphoglycerate dehydrogenase; 3 phosphoserine aminotransferase; phosphoserine phosphatase; or a multidrug transporter activity.

38. (canceled)

39. The method of claim 1, wherein the host is: a prokaryote selected from the group consisting of Escherichia; Clostridia; Corynebacteria; Cupriavidus; Pseudomonas; Delftia; Bacillus; Lactobacillus; Lactococcus; and Rhodococcus; or a eukaryote selected from the group consisting of Aspergillus, Saccharomyces, Pichia, Yarrowia, Issatchenkia, Debaryomyces, Arxula, and Kluyveromyces.

40. (canceled)

41. (canceled)

42. (canceled)

43. (canceled)

44. (canceled)

45. A recombinant host comprising an exogenous nucleic acid encoding a polypeptide having fatty acid O-methyltransferase activity, said host producing 2(E)-heptenedioate methyl ester; wherein optionally: the host further comprises an exogenous polypeptide having thioesterase or CoA-transferase activity and the host produces 2(E)-heptenedioate; the host further comprises an exogenous polypeptide having CoA ligase activity and the host produces 2(E)-heptendioyl-CoA methyl ester; host further comprises an exogenous polypeptide having trans-2-enoyl-CoA reductase activity and the host produces pimeloyl-CoA, adipyl-CoA methyl ester and/or an exogenous polypeptide having pimeloyl-[acp]methyl ester methylesterase activity; the host further comprises one or more exogenous polypeptides having homocitrate synthase, homocitrate dehydratase, homoaconitate hydratase, isohomocitrate dehydrogenase, decarboxylase, indolepyruvate decarboxylase, glutarate-semialdehyde dehydrogenase, or a glutarate:CoA ligase activity; the host further comprises one or more exogenous polypeptides selected from the group consisting of polypeptides having (a) .beta.-ketothiolase activity or acetyl-carboxylase activity in combination with acetoacetyl-CoA synthase activity, (b) 3-hydroxybutyryl-CoA dehydrogenase activity, (c) enoyl-CoA hydratase activity, and either (d) glutaryl-CoA dehydrogenase activity in combination with enoyl-CoA reductase activity or trans-2-enoyl-CoA reductase activity or (e) glutaconyl-CoA decarboxylase activity; the host further comprises one or more exogenous polypeptides having homocitrate synthase, homocitrate dehydratase, homoaconitate hydratase, isohomocitrate dehydrogenase, 2-hydroxyglutarate dehydrogenase, glutaconate CoA-transferase, or 2-hydroxyglutaryl-CoA dehydratase activity; or the host further comprises one or more exogenous polypeptides having glutarate semialdehyde dehydrogenase, 4-hydroxy-2-oxoheptanedioate aldolase, 2-oxo-hept-3-ene-1,7-dioate hydratase, 2-enoate reductase, 2-hydroxyglutarate dehydrogenase, glutaconate CoA-transferase, or 2-hydroxyglutaryl-CoA dehydratase activity.

46. (canceled)

47. (canceled)

48. (canceled)

49. (canceled)

50. (canceled)

51. The recombinant host of claim 45, said host further comprising one or more exogenous polypeptides having (i) .beta.-ketoacyl-[acp]synthase activity or .beta.-ketothiolase activity, (ii) 3-hydroxyacid-CoA dehydrogenase activity, and (iii) .beta.-hydroxyacid dehydrase activity.

52. (canceled)

53. (canceled)

54. The recombinant host of claim 45, said host further comprising one or more exogenous polypeptides having thioesterase, aldehyde dehydrogenase, 7-oxoheptanoate dehydrogenase, 6-oxohexanoate dehydrogenase, glutaconate CoA-transferase, reversible succinyl-CoA ligase, acetylating aldehyde dehydrogenase, or carboxylate reductase enhanced by phosphopantetheinyl transferase activity, said host further producing pimelic acid or pimelate semialdehyde.

55. The recombinant host of claim 54, said host further comprising: an exogenous polypeptide having .omega.-transaminase activity and said host further produces 7-aminoheptanoate; or one or more exogenous polypeptides having .omega.-transaminase, deacetylase, N-acetyl transferase, carboxylate reductase enhanced by phosphopantetheinyl transferase activity, or alcohol dehydrogenase activity, said host further producing heptamethylenediamine.

56. The recombinant host of claim 54, said host further comprising one or more exogenous polypeptides having 4-hydroxybutyrate dehydrogenase, 5-hydroxypentanoate dehydrogenase, 6-hydroxyhexanoate dehydrogenase, or alcohol dehydrogenase activity, said host further producing 7-hydroxyheptanoic acid, wherein the host optionally further comprises one or more exogenous polypeptides having (a) carboxylate reductase activity enhanced by phosphopantetheinyl transferase activity, and (b) alcohol dehydrogenase activity and the host further produces 1,7-heptanediol.

57. (canceled)

58. (canceled)

59. The method of claim 23, wherein: said polypeptide having carboxylate reductase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NOs: 7 to 12; said polypeptide having .omega.-transaminase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NOs: 13 to 18; said polypeptide having CoA ligase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 22 or SEQ ID NO: 23; said polypeptide having trans-2-enoyl-CoA reductase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 26 or SEQ ID NO: 27; said polypeptide having thioesterase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 21; and said polypeptide having .beta.-ketothiolase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NOs: 28 to 40.

60. (canceled)

61. (canceled)

62. (canceled)

63. (canceled)

64. (canceled)

65. A bio-derived product, bio-based product or fermentation-derived product, wherein said product comprises: i. a composition comprising at least one bio-derived, bio-based or fermentation-derived compound according to claim 1, ii. a bio-derived, bio-based or fermentation-derived polymer comprising the bio-derived, bio-based or fermentation-derived composition or compound of i., or a combination thereof, iii. a bio-derived, bio-based or fermentation-derived resin comprising the bio-derived, bio-based or fermentation-derived compound or bio-derived, bio-based or fermentation-derived composition of i. or any combination thereof or the bio-derived, bio-based or fermentation-derived polymer of ii. or a combination thereof, iv. a molded substance obtained by molding the bio-derived, bio-based or fermentation-derived polymer of ii. or the bio-derived, bio-based or fermentation-derived resin of iii., or a combination thereof, v. a bio-derived, bio-based or fermentation-derived formulation comprising the bio-derived, bio-based or fermentation-derived composition of i., bio-derived, bio-based or fermentation-derived compound of i., bio-derived, bio-based or fermentation-derived polymer of ii., bio-derived, bio-based or fermentation-derived resin of iii., or bio-derived, bio-based or fermentation-derived molded substance of iv, or a combination thereof, or vi. a bio-derived, bio-based or fermentation-derived semi-solid or a non-semi-solid stream, comprising the bio-derived, bio-based or fermentation-derived composition of i., bio-derived, bio-based or fermentation-derived compound of i., bio-derived, bio-based or fermentation-derived polymer of ii., bio-derived, bio-based or fermentation-derived resin of iii., bio-derived, bio-based or fermentation-derived formulation of v., or bio-derived, bio-based or fermentation-derived molded substance of iv., or a combination thereof.